diff --git a/platform/workspaceModel/jps/src/com/intellij/workspaceModel/ide/impl/jps/serialization/ModuleImlFileEntitiesSerializer.kt b/platform/workspaceModel/jps/src/com/intellij/workspaceModel/ide/impl/jps/serialization/ModuleImlFileEntitiesSerializer.kt
index 1a157d34fca8..005e2ccdd36a 100644
--- a/platform/workspaceModel/jps/src/com/intellij/workspaceModel/ide/impl/jps/serialization/ModuleImlFileEntitiesSerializer.kt
+++ b/platform/workspaceModel/jps/src/com/intellij/workspaceModel/ide/impl/jps/serialization/ModuleImlFileEntitiesSerializer.kt
@@ -595,75 +595,80 @@ internal open class ModuleImlFileEntitiesSerializer(internal val modulePath: Mod
     return result
   }
 
-@Suppress("UNCHECKED_CAST")
-override fun saveEntities(mainEntities: Collection<ModuleEntity>,
-                          entities: Map<Class<out WorkspaceEntity>, List<WorkspaceEntity>>,
-                          storage: EntityStorage,
-                          writer: JpsFileContentWriter) {
+  @Suppress("UNCHECKED_CAST")
+  override fun saveEntities(mainEntities: Collection<ModuleEntity>,
+                            entities: Map<Class<out WorkspaceEntity>, List<WorkspaceEntity>>,
+                            storage: EntityStorage,
+                            writer: JpsFileContentWriter) {
     val module = mainEntities.singleOrNull()
     if (module != null && acceptsSource(module.entitySource)) {
       saveModuleEntities(module, entities, storage, writer)
     }
-  else {
-    val targetComponent = if (Orphanage.use) ADDITIONAL_MODULE_ELEMENTS_COMPONENT_NAME else MODULE_ROOT_MANAGER_COMPONENT_NAME
-    if (ContentRootEntity::class.java in entities || SourceRootEntity::class.java in entities || ExcludeUrlEntity::class.java in entities) {
-      val contentEntities = entities[ContentRootEntity::class.java] as? List<ContentRootEntity> ?: emptyList()
-      val sourceRootEntities = (entities[SourceRootEntity::class.java] as? List<SourceRootEntity>)?.toMutableSet() ?: mutableSetOf()
-      val excludeRoots = (entities[ExcludeUrlEntity::class.java] as? List<ExcludeUrlEntity>)?.filter { it.contentRoot != null }?.toMutableSet()
-                         ?: mutableSetOf()
-      val rootElement = JDomSerializationUtil.createComponentElement(targetComponent)
-      if (contentEntities.isNotEmpty()) {
-        contentEntities.forEach {
-          it.sourceRoots.filter { sourceRootEntity -> acceptsSource(sourceRootEntity.entitySource) }.forEach { sourceRootEntity ->
-            sourceRootEntities.remove(sourceRootEntity)
-          }
-          it.excludedUrls.filter { exclude -> acceptsSource(exclude.entitySource) }.forEach { exclude ->
-            excludeRoots.remove(exclude)
-          }
-        }
-        saveContentEntities(contentEntities, rootElement)
-        writer.saveComponent(fileUrl.url, targetComponent, rootElement)
-      }
-      if (sourceRootEntities.isNotEmpty() || excludeRoots.isNotEmpty()) {
-        val excludes = excludeRoots.groupBy { it.contentRoot!!.url }.toMutableMap()
-        if (sourceRootEntities.isNotEmpty()) {
-          sourceRootEntities.groupBy { it.contentRoot }
-            .toSortedMap(compareBy { it.url.url })
-            .forEach { (contentRoot, sourceRoots) ->
-              val contentRootTag = Element(CONTENT_TAG)
-              contentRootTag.setAttribute(URL_ATTRIBUTE, contentRoot.url.url)
-              if (Orphanage.use) {
-                contentRootTag.setAttribute(DUMB_ATTRIBUTE, true.toString())
-              }
-              saveSourceRootEntities(sourceRoots, contentRootTag, contentRoot.getSourceRootsComparator())
-              excludes[contentRoot.url]?.let {
-                saveExcludeUrls(contentRootTag, it)
-                excludes.remove(contentRoot.url)
-              }
-              rootElement.addContent(contentRootTag)
-              writer.saveComponent(fileUrl.url, targetComponent, rootElement)
+    else {
+      val targetComponent = if (Orphanage.use) ADDITIONAL_MODULE_ELEMENTS_COMPONENT_NAME else MODULE_ROOT_MANAGER_COMPONENT_NAME
+      if (ContentRootEntity::class.java in entities || SourceRootEntity::class.java in entities || ExcludeUrlEntity::class.java in entities) {
+        val contentEntities = entities[ContentRootEntity::class.java] as? List<ContentRootEntity> ?: emptyList()
+        val sourceRootEntities = (entities[SourceRootEntity::class.java] as? List<SourceRootEntity>)?.toMutableSet() ?: mutableSetOf()
+        val excludeRoots = (entities[ExcludeUrlEntity::class.java] as? List<ExcludeUrlEntity>)?.filter { it.contentRoot != null }?.toMutableSet()
+                           ?: mutableSetOf()
+        val rootElement = JDomSerializationUtil.createComponentElement(targetComponent)
+        if (contentEntities.isNotEmpty()) {
+          contentEntities.forEach {
+            it.sourceRoots.filter { sourceRootEntity -> acceptsSource(sourceRootEntity.entitySource) }.forEach { sourceRootEntity ->
+              sourceRootEntities.remove(sourceRootEntity)
+            }
+            it.excludedUrls.filter { exclude -> acceptsSource(exclude.entitySource) }.forEach { exclude ->
+              excludeRoots.remove(exclude)
             }
-        }
-        excludes.toSortedMap(compareBy { it.url }).forEach { (url, exclude) ->
-          val contentRootTag = Element(CONTENT_TAG)
-          contentRootTag.setAttribute(URL_ATTRIBUTE, url.url)
-          if (Orphanage.use) {
-            contentRootTag.setAttribute(DUMB_ATTRIBUTE, true.toString())
           }
-          saveExcludeUrls(contentRootTag, exclude)
-          rootElement.addContent(contentRootTag)
+          saveContentEntities(contentEntities, rootElement)
           writer.saveComponent(fileUrl.url, targetComponent, rootElement)
         }
-      }
+        if (sourceRootEntities.isNotEmpty() || excludeRoots.isNotEmpty()) {
+          val excludes = excludeRoots.groupBy { it.contentRoot!!.url }.toMutableMap()
+          if (sourceRootEntities.isNotEmpty()) {
+            sourceRootEntities.groupBy { it.contentRoot }
+              .toSortedMap(compareBy { it.url.url })
+              .forEach { (contentRoot, sourceRoots) ->
+                val contentRootTag = Element(CONTENT_TAG)
+                contentRootTag.setAttribute(URL_ATTRIBUTE, contentRoot.url.url)
+                if (Orphanage.use) {
+                  contentRootTag.setAttribute(DUMB_ATTRIBUTE, true.toString())
+                }
+                saveSourceRootEntities(sourceRoots, contentRootTag, contentRoot.getSourceRootsComparator())
+                excludes[contentRoot.url]?.let {
+                  saveExcludeUrls(contentRootTag, it)
+                  excludes.remove(contentRoot.url)
+                }
+                rootElement.addContent(contentRootTag)
+                writer.saveComponent(fileUrl.url, targetComponent, rootElement)
+              }
+          }
+          excludes.toSortedMap(compareBy { it.url }).forEach { (url, exclude) ->
+            val contentRootTag = Element(CONTENT_TAG)
+            contentRootTag.setAttribute(URL_ATTRIBUTE, url.url)
+            if (Orphanage.use) {
+              contentRootTag.setAttribute(DUMB_ATTRIBUTE, true.toString())
+            }
+            saveExcludeUrls(contentRootTag, exclude)
+            rootElement.addContent(contentRootTag)
+            writer.saveComponent(fileUrl.url, targetComponent, rootElement)
+          }
+        }
 
-    }
-    else {
-      writer.saveComponent(fileUrl.url, MODULE_ROOT_MANAGER_COMPONENT_NAME, null)
-      writer.saveComponent(fileUrl.url, DEPRECATED_MODULE_MANAGER_COMPONENT_NAME, null)
-      if (Orphanage.use) {
-        writer.saveComponent(fileUrl.url, ADDITIONAL_MODULE_ELEMENTS_COMPONENT_NAME, null)
+        if (Orphanage.use) {
+          // Component to save additional roots before introducing AdditionalModuleElements.
+          // It's not used for this function anymore and should be cleared
+          writer.saveComponent(fileUrl.url, MODULE_ROOT_MANAGER_COMPONENT_NAME, null)
+        }
+      }
+      else {
+        writer.saveComponent(fileUrl.url, MODULE_ROOT_MANAGER_COMPONENT_NAME, null)
+        writer.saveComponent(fileUrl.url, DEPRECATED_MODULE_MANAGER_COMPONENT_NAME, null)
+        if (Orphanage.use) {
+          writer.saveComponent(fileUrl.url, ADDITIONAL_MODULE_ELEMENTS_COMPONENT_NAME, null)
+        }
       }
-    }
     }
 
     createFacetSerializer().saveFacetEntities(module, entities, writer, this::acceptsSource)
@@ -1029,6 +1034,7 @@ internal open class ModuleListSerializerImpl(override val fileUrl: String,
     writer.saveComponent(fileUrl, MODULE_ROOT_MANAGER_COMPONENT_NAME, null)
     writer.saveComponent(fileUrl, DEPRECATED_MODULE_MANAGER_COMPONENT_NAME, null)
     writer.saveComponent(fileUrl, TEST_MODULE_PROPERTIES_COMPONENT_NAME, null)
+    writer.saveComponent(fileUrl, ADDITIONAL_MODULE_ELEMENTS_COMPONENT_NAME, null)
   }
 
   private fun getModuleFileUrl(source: JpsFileEntitySource.FileInDirectory,
diff --git a/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadAndRemoveAdditionalRootY/.idea/misc.xml b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadAndRemoveAdditionalRootY/.idea/misc.xml
new file mode 100644
index 000000000000..8ddc2148d7dc
--- /dev/null
+++ b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadAndRemoveAdditionalRootY/.idea/misc.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ExternalStorageConfigurationManager" enabled="true" />
+  <component name="ProjectRootManager" version="2" languageLevel="JDK_1_8" />
+</project>
\ No newline at end of file
diff --git a/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadAndRemoveAdditionalRootY/.idea/modules.xml b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadAndRemoveAdditionalRootY/.idea/modules.xml
new file mode 100644
index 000000000000..7c5c7c342a23
--- /dev/null
+++ b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadAndRemoveAdditionalRootY/.idea/modules.xml
@@ -0,0 +1 @@
+<delete/>
\ No newline at end of file
diff --git a/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadAndRemoveAdditionalRootY/cache/modules/test.xml b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadAndRemoveAdditionalRootY/cache/modules/test.xml
new file mode 100644
index 000000000000..a2fd710158f0
--- /dev/null
+++ b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadAndRemoveAdditionalRootY/cache/modules/test.xml
@@ -0,0 +1,7 @@
+<module version="4">
+  <component name="ExternalSystem" externalSystem="GRADLE" externalSystemModuleGroup="group" externalSystemModuleVersion="42.0" linkedProjectId="test" linkedProjectPath="$MODULE_DIR$" rootProjectPath="$MODULE_DIR$" />
+  <component name="NewModuleRootManager" inherit-compiler-output="true">
+    <exclude-output />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+</module>
\ No newline at end of file
diff --git a/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadAndRemoveAdditionalRootY/cache/project/modules.xml b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadAndRemoveAdditionalRootY/cache/project/modules.xml
new file mode 100644
index 000000000000..4559fe912c0c
--- /dev/null
+++ b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadAndRemoveAdditionalRootY/cache/project/modules.xml
@@ -0,0 +1,7 @@
+<project version="4">
+  <component name="ExternalProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/test.iml" filepath="$PROJECT_DIR$/test.iml" />
+    </modules>
+  </component>
+</project>
\ No newline at end of file
diff --git a/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadAndRemoveAdditionalRootY/test.iml b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadAndRemoveAdditionalRootY/test.iml
new file mode 100644
index 000000000000..7c5c7c342a23
--- /dev/null
+++ b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadAndRemoveAdditionalRootY/test.iml
@@ -0,0 +1 @@
+<delete/>
\ No newline at end of file
diff --git a/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadIncorrectSavedAdditionalRoots/.idea/misc.xml b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadIncorrectSavedAdditionalRoots/.idea/misc.xml
new file mode 100644
index 000000000000..8ddc2148d7dc
--- /dev/null
+++ b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadIncorrectSavedAdditionalRoots/.idea/misc.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ExternalStorageConfigurationManager" enabled="true" />
+  <component name="ProjectRootManager" version="2" languageLevel="JDK_1_8" />
+</project>
\ No newline at end of file
diff --git a/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadIncorrectSavedAdditionalRoots/.idea/modules.xml b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadIncorrectSavedAdditionalRoots/.idea/modules.xml
new file mode 100644
index 000000000000..b402e967f73f
--- /dev/null
+++ b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadIncorrectSavedAdditionalRoots/.idea/modules.xml
@@ -0,0 +1,7 @@
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/test.iml" filepath="$PROJECT_DIR$/test.iml" />
+    </modules>
+  </component>
+</project>
\ No newline at end of file
diff --git a/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadIncorrectSavedAdditionalRoots/cache/modules/test.xml b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadIncorrectSavedAdditionalRoots/cache/modules/test.xml
new file mode 100644
index 000000000000..a2fd710158f0
--- /dev/null
+++ b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadIncorrectSavedAdditionalRoots/cache/modules/test.xml
@@ -0,0 +1,7 @@
+<module version="4">
+  <component name="ExternalSystem" externalSystem="GRADLE" externalSystemModuleGroup="group" externalSystemModuleVersion="42.0" linkedProjectId="test" linkedProjectPath="$MODULE_DIR$" rootProjectPath="$MODULE_DIR$" />
+  <component name="NewModuleRootManager" inherit-compiler-output="true">
+    <exclude-output />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+</module>
\ No newline at end of file
diff --git a/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadIncorrectSavedAdditionalRoots/cache/project/modules.xml b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadIncorrectSavedAdditionalRoots/cache/project/modules.xml
new file mode 100644
index 000000000000..4559fe912c0c
--- /dev/null
+++ b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadIncorrectSavedAdditionalRoots/cache/project/modules.xml
@@ -0,0 +1,7 @@
+<project version="4">
+  <component name="ExternalProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/test.iml" filepath="$PROJECT_DIR$/test.iml" />
+    </modules>
+  </component>
+</project>
\ No newline at end of file
diff --git a/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadIncorrectSavedAdditionalRoots/test.iml b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadIncorrectSavedAdditionalRoots/test.iml
new file mode 100644
index 000000000000..f92789a4c813
--- /dev/null
+++ b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/after/loadIncorrectSavedAdditionalRoots/test.iml
@@ -0,0 +1,5 @@
+<module version="4">
+  <component name="AdditionalModuleElements">
+    <content url="file://$MODULE_DIR$/myContentRoot" />
+  </component>
+</module>
\ No newline at end of file
diff --git a/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadAndRemoveAdditionalRoot/.idea/misc.xml b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadAndRemoveAdditionalRoot/.idea/misc.xml
new file mode 100644
index 000000000000..8ddc2148d7dc
--- /dev/null
+++ b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadAndRemoveAdditionalRoot/.idea/misc.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ExternalStorageConfigurationManager" enabled="true" />
+  <component name="ProjectRootManager" version="2" languageLevel="JDK_1_8" />
+</project>
\ No newline at end of file
diff --git a/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadAndRemoveAdditionalRoot/.idea/modules.xml b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadAndRemoveAdditionalRoot/.idea/modules.xml
new file mode 100644
index 000000000000..b402e967f73f
--- /dev/null
+++ b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadAndRemoveAdditionalRoot/.idea/modules.xml
@@ -0,0 +1,7 @@
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/test.iml" filepath="$PROJECT_DIR$/test.iml" />
+    </modules>
+  </component>
+</project>
\ No newline at end of file
diff --git a/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadAndRemoveAdditionalRoot/cache/modules/test.xml b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadAndRemoveAdditionalRoot/cache/modules/test.xml
new file mode 100644
index 000000000000..a2fd710158f0
--- /dev/null
+++ b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadAndRemoveAdditionalRoot/cache/modules/test.xml
@@ -0,0 +1,7 @@
+<module version="4">
+  <component name="ExternalSystem" externalSystem="GRADLE" externalSystemModuleGroup="group" externalSystemModuleVersion="42.0" linkedProjectId="test" linkedProjectPath="$MODULE_DIR$" rootProjectPath="$MODULE_DIR$" />
+  <component name="NewModuleRootManager" inherit-compiler-output="true">
+    <exclude-output />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+</module>
\ No newline at end of file
diff --git a/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadAndRemoveAdditionalRoot/cache/project/modules.xml b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadAndRemoveAdditionalRoot/cache/project/modules.xml
new file mode 100644
index 000000000000..4559fe912c0c
--- /dev/null
+++ b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadAndRemoveAdditionalRoot/cache/project/modules.xml
@@ -0,0 +1,7 @@
+<project version="4">
+  <component name="ExternalProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/test.iml" filepath="$PROJECT_DIR$/test.iml" />
+    </modules>
+  </component>
+</project>
\ No newline at end of file
diff --git a/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadAndRemoveAdditionalRoot/test.iml b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadAndRemoveAdditionalRoot/test.iml
new file mode 100644
index 000000000000..f92789a4c813
--- /dev/null
+++ b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadAndRemoveAdditionalRoot/test.iml
@@ -0,0 +1,5 @@
+<module version="4">
+  <component name="AdditionalModuleElements">
+    <content url="file://$MODULE_DIR$/myContentRoot" />
+  </component>
+</module>
\ No newline at end of file
diff --git a/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadIncorrectSavedAdditionalRoots/.idea/misc.xml b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadIncorrectSavedAdditionalRoots/.idea/misc.xml
new file mode 100644
index 000000000000..8ddc2148d7dc
--- /dev/null
+++ b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadIncorrectSavedAdditionalRoots/.idea/misc.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ExternalStorageConfigurationManager" enabled="true" />
+  <component name="ProjectRootManager" version="2" languageLevel="JDK_1_8" />
+</project>
\ No newline at end of file
diff --git a/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadIncorrectSavedAdditionalRoots/.idea/modules.xml b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadIncorrectSavedAdditionalRoots/.idea/modules.xml
new file mode 100644
index 000000000000..b402e967f73f
--- /dev/null
+++ b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadIncorrectSavedAdditionalRoots/.idea/modules.xml
@@ -0,0 +1,7 @@
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/test.iml" filepath="$PROJECT_DIR$/test.iml" />
+    </modules>
+  </component>
+</project>
\ No newline at end of file
diff --git a/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadIncorrectSavedAdditionalRoots/cache/modules/test.xml b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadIncorrectSavedAdditionalRoots/cache/modules/test.xml
new file mode 100644
index 000000000000..a2fd710158f0
--- /dev/null
+++ b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadIncorrectSavedAdditionalRoots/cache/modules/test.xml
@@ -0,0 +1,7 @@
+<module version="4">
+  <component name="ExternalSystem" externalSystem="GRADLE" externalSystemModuleGroup="group" externalSystemModuleVersion="42.0" linkedProjectId="test" linkedProjectPath="$MODULE_DIR$" rootProjectPath="$MODULE_DIR$" />
+  <component name="NewModuleRootManager" inherit-compiler-output="true">
+    <exclude-output />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+</module>
\ No newline at end of file
diff --git a/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadIncorrectSavedAdditionalRoots/cache/project/modules.xml b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadIncorrectSavedAdditionalRoots/cache/project/modules.xml
new file mode 100644
index 000000000000..4559fe912c0c
--- /dev/null
+++ b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadIncorrectSavedAdditionalRoots/cache/project/modules.xml
@@ -0,0 +1,7 @@
+<project version="4">
+  <component name="ExternalProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/test.iml" filepath="$PROJECT_DIR$/test.iml" />
+    </modules>
+  </component>
+</project>
\ No newline at end of file
diff --git a/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadIncorrectSavedAdditionalRoots/test.iml b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadIncorrectSavedAdditionalRoots/test.iml
new file mode 100644
index 000000000000..24844a0d3990
--- /dev/null
+++ b/platform/workspaceModel/jps/tests/testData/serialization/splitModuleAndContentRoot/before/loadIncorrectSavedAdditionalRoots/test.iml
@@ -0,0 +1,5 @@
+<module version="4">
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$/myContentRoot" />
+  </component>
+</module>
\ No newline at end of file
diff --git a/platform/workspaceModel/jps/tests/testSrc/com/intellij/workspaceModel/ide/impl/jps/serialization/JpsSplitModuleAndContentRootTest.kt b/platform/workspaceModel/jps/tests/testSrc/com/intellij/workspaceModel/ide/impl/jps/serialization/JpsSplitModuleAndContentRootTest.kt
index f94bfcd3cb59..6a812b41a9b7 100644
--- a/platform/workspaceModel/jps/tests/testSrc/com/intellij/workspaceModel/ide/impl/jps/serialization/JpsSplitModuleAndContentRootTest.kt
+++ b/platform/workspaceModel/jps/tests/testSrc/com/intellij/workspaceModel/ide/impl/jps/serialization/JpsSplitModuleAndContentRootTest.kt
@@ -33,6 +33,7 @@ class JpsSplitModuleAndContentRootTest {
 
   @Before
   fun setUp() {
+    Assume.assumeTrue(Orphanage.use)
     virtualFileManager = IdeVirtualFileUrlManagerImpl()
   }
 
@@ -48,7 +49,6 @@ class JpsSplitModuleAndContentRootTest {
 
   @Test
   fun `add local content root via orphanage`() {
-    Assume.assumeTrue(Orphanage.use)
     checkSaveProjectAfterChange("after/addContentRootOrphanage", "after/addContentRootOrphanage", false) { builder, orphanage, configLocation ->
       assertTrue(builder.entities(ModuleEntity::class.java).toList().isEmpty())
       assertTrue(orphanage.entities(ModuleEntity::class.java).single().contentRoots.single().entitySource !is OrphanageWorkerEntitySource)
@@ -576,9 +576,25 @@ class JpsSplitModuleAndContentRootTest {
     }
   }
 
+  @Test
+  fun `load incorrect saved additional root`() {
+    checkSaveProjectAfterChange("before/loadIncorrectSavedAdditionalRoots", "after/loadIncorrectSavedAdditionalRoots", forceFilesRewrite = true) { builder, orphanage, configLocation ->
+      // Nothing
+    }
+  }
+
+  @Test
+  fun `load and remove additional root`() {
+    checkSaveProjectAfterChange("before/loadAndRemoveAdditionalRoot", "after/loadAndRemoveAdditionalRootY", forceFilesRewrite = true) { builder, orphanage, configLocation ->
+      val toRemove = builder.entities(ModuleEntity::class.java).single().contentRoots.filter { it.entitySource !is JpsImportedEntitySource }
+      toRemove.forEach { builder.removeEntity(it) }
+    }
+  }
+
   private fun checkSaveProjectAfterChange(dirBefore: String,
                                           dirAfter: String,
                                           externalStorage: Boolean = true,
+                                          forceFilesRewrite: Boolean = false,
                                           change: (MutableEntityStorage, MutableEntityStorage, JpsProjectConfigLocation) -> Unit) {
 
     val initialDir = PathManagerEx.findFileUnderCommunityHome(
@@ -588,7 +604,7 @@ class JpsSplitModuleAndContentRootTest {
     checkSaveProjectAfterChange(initialDir, dirAfter, { builder, orphanage, _, location -> change(builder, orphanage, location) },
                                 emptySet(),
                                 virtualFileManager, "serialization/splitModuleAndContentRoot", false,
-                                externalStorageConfigurationManager)
+                                externalStorageConfigurationManager, forceAllFilesRewrite = forceFilesRewrite)
   }
 
   companion object {