diff --git a/platform/workspaceModel/storage/src/com/intellij/workspaceModel/storage/impl/StorageIndexes.kt b/platform/workspaceModel/storage/src/com/intellij/workspaceModel/storage/impl/StorageIndexes.kt
index e0d89890f0dd..79880684f1d4 100644
--- a/platform/workspaceModel/storage/src/com/intellij/workspaceModel/storage/impl/StorageIndexes.kt
+++ b/platform/workspaceModel/storage/src/com/intellij/workspaceModel/storage/impl/StorageIndexes.kt
@@ -136,6 +136,18 @@ internal class MutableStorageIndexes(
     persistentIdIndex.index(entityId)
   }
 
+  fun <T : WorkspaceEntity> simpleUpdateSoftReferences(copiedData: WorkspaceEntityData<T>) {
+    val pid = copiedData.createPid()
+    if (copiedData is SoftLinkable) {
+      val beforeSoftLinks = HashSet(this.softLinks.getKeys(pid))
+      val afterSoftLinks = copiedData.getLinks()
+      if (beforeSoftLinks != afterSoftLinks) {
+        beforeSoftLinks.forEach { this.softLinks.remove(it, pid) }
+        afterSoftLinks.forEach { this.softLinks.put(it, pid) }
+      }
+    }
+  }
+
   @OptIn(ExperimentalStdlibApi::class)
   fun <T : WorkspaceEntity> updateSoftReferences(beforePersistentId: PersistentEntityId<*>?,
                                                  copiedData: WorkspaceEntityData<T>,
diff --git a/platform/workspaceModel/storage/src/com/intellij/workspaceModel/storage/impl/WorkspaceEntityStorageImpl.kt b/platform/workspaceModel/storage/src/com/intellij/workspaceModel/storage/impl/WorkspaceEntityStorageImpl.kt
index a789c7db1a7b..f872649886dc 100644
--- a/platform/workspaceModel/storage/src/com/intellij/workspaceModel/storage/impl/WorkspaceEntityStorageImpl.kt
+++ b/platform/workspaceModel/storage/src/com/intellij/workspaceModel/storage/impl/WorkspaceEntityStorageImpl.kt
@@ -121,15 +121,11 @@ internal class WorkspaceEntityStorageBuilderImpl(
     }
 
     // Add an entry to changelog
-    val pid = e.id
-    val parents = this.refs.getParentRefsOfChild(pid)
-    val children = this.refs.getChildrenRefsOfParentBy(pid)
-    updateChangeLog { it.add(ChangeEntry.ReplaceEntity(copiedData, children, parents)) }
+    addReplaceChange(copiedData)
 
     val updatedEntity = copiedData.createEntity(this)
 
-    if (updatedEntity is WorkspaceEntityWithPersistentId) indexes.persistentIdIndex.index(pid, updatedEntity.persistentId())
-    indexes.updateSoftReferences(beforePersistentId, copiedData, this)
+    updatePersistentIdIndexes(updatedEntity, beforePersistentId, copiedData)
 
     // Assert consistency
     this.assertConsistencyInStrictMode()
@@ -137,6 +133,41 @@ internal class WorkspaceEntityStorageBuilderImpl(
     return updatedEntity
   }
 
+  private fun <T : WorkspaceEntity> updatePersistentIdIndexes(updatedEntity: WorkspaceEntity,
+                                                              beforePersistentId: PersistentEntityId<*>?,
+                                                              copiedData: WorkspaceEntityData<T>) {
+    val pid = (updatedEntity as WorkspaceEntityBase).id
+    if (updatedEntity is WorkspaceEntityWithPersistentId) {
+      val newPersistentId = updatedEntity.persistentId()
+      if (beforePersistentId != null && beforePersistentId != newPersistentId) {
+        indexes.persistentIdIndex.index(pid, newPersistentId)
+        updateComposedIds(beforePersistentId, newPersistentId)
+      }
+    }
+    indexes.simpleUpdateSoftReferences(copiedData)
+  }
+
+  private fun updateComposedIds(beforePersistentId: PersistentEntityId<*>, newPersistentId: PersistentEntityId<*> ) {
+    val idsWithSoftRef = HashSet(indexes.softLinks.getValues(beforePersistentId))
+    for (entityId in idsWithSoftRef) {
+      val entity = this.entitiesByType.getEntityDataForModification(entityId)
+      val editingBeforePersistentId = entity.persistentId(this)
+      (entity as SoftLinkable).updateLink(beforePersistentId, newPersistentId, ArrayList())
+
+      // Add an entry to changelog
+      addReplaceChange(entity)
+
+      updatePersistentIdIndexes(entity.createEntity(this), editingBeforePersistentId, entity)
+    }
+  }
+
+  private fun addReplaceChange(entity: WorkspaceEntityData<*>) {
+    val pid = entity.createPid()
+    val parents = this.refs.getParentRefsOfChild(pid)
+    val children = this.refs.getChildrenRefsOfParentBy(pid)
+    updateChangeLog { it.add(ChangeEntry.ReplaceEntity(entity, children, parents)) }
+  }
+
   override fun <T : WorkspaceEntity> changeSource(e: T, newSource: EntitySource): T {
     val copiedData = entitiesByType.getEntityDataForModification((e as WorkspaceEntityBase).id) as WorkspaceEntityData<T>
     copiedData.entitySource = newSource