diff --git a/jps/jps-builders/src/org/jetbrains/jps/backwardRefs/BackwardReferenceIndexWriter.java b/jps/jps-builders/src/org/jetbrains/jps/backwardRefs/BackwardReferenceIndexWriter.java
index 564e2ee17ba1..bba1c105a7ec 100644
--- a/jps/jps-builders/src/org/jetbrains/jps/backwardRefs/BackwardReferenceIndexWriter.java
+++ b/jps/jps-builders/src/org/jetbrains/jps/backwardRefs/BackwardReferenceIndexWriter.java
@@ -263,7 +263,7 @@ public class BackwardReferenceIndexWriter {
     if (oldSuperClasses != null && !oldSuperClasses.isEmpty()) {
       myIndex.getHierarchyMap().removeAll(classId, oldSuperClasses);
       for (LightRef anOldClass : oldSuperClasses) {
-        myIndex.getBackwardHierarchyMap().put(anOldClass, classId);
+        myIndex.getBackwardHierarchyMap().removeFrom(anOldClass, classId);
       }
     }
   }
diff --git a/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate/afterSecondMakeIndex.txt b/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate/afterSecondMakeIndex.txt
index b0aa10f4597b..c5da730e5778 100644
--- a/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate/afterSecondMakeIndex.txt
+++ b/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate/afterSecondMakeIndex.txt
@@ -1,5 +1,4 @@
 Backward Hierarchy:
-Foo -> FooImpl
 java.lang.Object -> Bar FooImpl
 
 Backward References:
diff --git a/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate2/Bar.java b/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate2/Bar.java
new file mode 100644
index 000000000000..37b4129a65a5
--- /dev/null
+++ b/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate2/Bar.java
@@ -0,0 +1,9 @@
+import java.util.Collections;
+
+abstract class Foo {
+
+  void m() {
+    Collections.emptySet();
+  }
+
+}
\ No newline at end of file
diff --git a/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate2/Foo.java b/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate2/Foo.java
new file mode 100644
index 000000000000..574d3e31f294
--- /dev/null
+++ b/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate2/Foo.java
@@ -0,0 +1,10 @@
+import java.util.Collections;
+import java.util.List;
+
+abstract class Foo implements List {
+
+  void m() {
+    Collections.emptyList();
+  }
+
+}
\ No newline at end of file
diff --git a/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate2/Foo_2.java b/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate2/Foo_2.java
new file mode 100644
index 000000000000..37b4129a65a5
--- /dev/null
+++ b/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate2/Foo_2.java
@@ -0,0 +1,9 @@
+import java.util.Collections;
+
+abstract class Foo {
+
+  void m() {
+    Collections.emptySet();
+  }
+
+}
\ No newline at end of file
diff --git a/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate2/after1MakeIndex.txt b/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate2/after1MakeIndex.txt
new file mode 100644
index 000000000000..88bcc80abf04
--- /dev/null
+++ b/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate2/after1MakeIndex.txt
@@ -0,0 +1,13 @@
+Backward Hierarchy:
+java.lang.Object -> Foo
+
+Backward References:
+Foo in Foo
+Foo.<init>(0) in Foo
+Foo.m(0) in Foo
+java.lang.Object.<init>(0) in Foo
+java.util.Collections in Foo
+java.util.Collections.emptySet(0) in Foo
+
+Class Definitions:
+Foo in Foo
\ No newline at end of file
diff --git a/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate2/after2MakeIndex.txt b/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate2/after2MakeIndex.txt
new file mode 100644
index 000000000000..89204bcd0cc3
--- /dev/null
+++ b/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate2/after2MakeIndex.txt
@@ -0,0 +1,13 @@
+Backward Hierarchy:
+java.lang.Object -> Foo
+
+Backward References:
+Foo in Bar
+Foo.<init>(0) in Bar
+Foo.m(0) in Bar
+java.lang.Object.<init>(0) in Bar
+java.util.Collections in Bar
+java.util.Collections.emptySet(0) in Bar
+
+Class Definitions:
+Foo in Bar
\ No newline at end of file
diff --git a/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate2/initialIndex.txt b/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate2/initialIndex.txt
new file mode 100644
index 000000000000..f33fab5189e8
--- /dev/null
+++ b/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate2/initialIndex.txt
@@ -0,0 +1,15 @@
+Backward Hierarchy:
+java.lang.Object -> Foo
+java.util.List -> Foo
+
+Backward References:
+Foo in Foo
+Foo.<init>(0) in Foo
+Foo.m(0) in Foo
+java.lang.Object.<init>(0) in Foo
+java.util.Collections in Foo
+java.util.Collections.emptyList(0) in Foo
+java.util.List in Foo
+
+Class Definitions:
+Foo in Foo
\ No newline at end of file
diff --git a/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate3/Bar.java b/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate3/Bar.java
new file mode 100644
index 000000000000..b8ec8acd55c0
--- /dev/null
+++ b/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate3/Bar.java
@@ -0,0 +1,9 @@
+import java.util.Collections;
+
+class Bar {
+
+  void m() {
+    Collections.emptySet();
+  }
+
+}
\ No newline at end of file
diff --git a/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate3/Foo.java b/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate3/Foo.java
new file mode 100644
index 000000000000..8e97f294cb51
--- /dev/null
+++ b/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate3/Foo.java
@@ -0,0 +1,17 @@
+import java.util.Collections;
+
+class Foo {
+
+  void m() {
+    Collections.emptyList();
+  }
+
+}
+
+class Bar {
+
+  void m() {
+    Collections.emptySet();
+  }
+
+}
\ No newline at end of file
diff --git a/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate3/Foo_2.java b/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate3/Foo_2.java
new file mode 100644
index 000000000000..44aa2d59a7aa
--- /dev/null
+++ b/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate3/Foo_2.java
@@ -0,0 +1,9 @@
+import java.util.Collections;
+
+class Foo {
+
+  void m() {
+    Collections.emptyList();
+  }
+
+}
\ No newline at end of file
diff --git a/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate3/after1MakeIndex.txt b/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate3/after1MakeIndex.txt
new file mode 100644
index 000000000000..9cdfb274efb7
--- /dev/null
+++ b/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate3/after1MakeIndex.txt
@@ -0,0 +1,18 @@
+Backward Hierarchy:
+java.lang.Object -> Bar Foo
+
+Backward References:
+Bar in Bar
+Bar.<init>(0) in Bar
+Bar.m(0) in Bar
+Foo in Foo
+Foo.<init>(0) in Foo
+Foo.m(0) in Foo
+java.lang.Object.<init>(0) in Bar Foo
+java.util.Collections in Bar Foo
+java.util.Collections.emptyList(0) in Foo
+java.util.Collections.emptySet(0) in Bar
+
+Class Definitions:
+Bar in Bar
+Foo in Foo
\ No newline at end of file
diff --git a/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate3/initialIndex.txt b/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate3/initialIndex.txt
new file mode 100644
index 000000000000..4379394b3c66
--- /dev/null
+++ b/jps/jps-builders/testData/referencesIndex/incrementalIndexUpdate3/initialIndex.txt
@@ -0,0 +1,18 @@
+Backward Hierarchy:
+java.lang.Object -> Bar Foo
+
+Backward References:
+Bar in Foo
+Bar.<init>(0) in Foo
+Bar.m(0) in Foo
+Foo in Foo
+Foo.<init>(0) in Foo
+Foo.m(0) in Foo
+java.lang.Object.<init>(0) in Foo
+java.util.Collections in Foo
+java.util.Collections.emptyList(0) in Foo
+java.util.Collections.emptySet(0) in Foo
+
+Class Definitions:
+Bar in Foo
+Foo in Foo
\ No newline at end of file
diff --git a/jps/jps-builders/testSrc/org/jetbrains/references/ReferenceIndexTest.kt b/jps/jps-builders/testSrc/org/jetbrains/references/ReferenceIndexTest.kt
index ad92bd979c2f..13d667071be9 100644
--- a/jps/jps-builders/testSrc/org/jetbrains/references/ReferenceIndexTest.kt
+++ b/jps/jps-builders/testSrc/org/jetbrains/references/ReferenceIndexTest.kt
@@ -33,6 +33,25 @@ class ReferenceIndexTest : ReferenceIndexTestBase() {
     assertIndexEquals("afterSecondMakeIndex.txt")
   }
 
+  fun testIncrementalIndexUpdate2() {
+    assertIndexOnRebuild("Foo.java")
+    changeFileContent("Foo.java", "Foo_2.java")
+    buildAllModules()
+    assertIndexEquals("after1MakeIndex.txt")
+    deleteFile("m/Foo.java")
+    addFile("Bar.java")
+    buildAllModules()
+    assertIndexEquals("after2MakeIndex.txt")
+  }
+
+  fun testIncrementalIndexUpdate3() {
+    assertIndexOnRebuild("Foo.java")
+    changeFileContent("Foo.java", "Foo_2.java")
+    addFile("Bar.java")
+    buildAllModules()
+    assertIndexEquals("after1MakeIndex.txt")
+  }
+
   fun testFileCaseOnlyRename() {
     assertIndexOnRebuild("Bar.java")
     renameFile("Bar.java", "bar.java")