diff --git a/platform/workspace/storage/src/com/intellij/platform/workspace/storage/impl/ConsistencyChecker.kt b/platform/workspace/storage/src/com/intellij/platform/workspace/storage/impl/ConsistencyChecker.kt
index 9c65320554a5..e08c26237646 100644
--- a/platform/workspace/storage/src/com/intellij/platform/workspace/storage/impl/ConsistencyChecker.kt
+++ b/platform/workspace/storage/src/com/intellij/platform/workspace/storage/impl/ConsistencyChecker.kt
@@ -35,6 +35,8 @@ internal fun AbstractEntityStorage.assertConsistency() {
     if (!connectionId.isParentNullable) {
       checkStrongConnection(this, map.keys, connectionId.childClass, connectionId.parentClass, connectionId)
     }
+
+    map.assertConsistency()
   }
 
   refs.oneToOneContainer.forEach { (connectionId, map) ->
diff --git a/platform/workspace/storage/src/com/intellij/platform/workspace/storage/impl/RefsTable.kt b/platform/workspace/storage/src/com/intellij/platform/workspace/storage/impl/RefsTable.kt
index 8fed795e9459..0eba087e0d28 100644
--- a/platform/workspace/storage/src/com/intellij/platform/workspace/storage/impl/RefsTable.kt
+++ b/platform/workspace/storage/src/com/intellij/platform/workspace/storage/impl/RefsTable.kt
@@ -439,7 +439,8 @@ internal class MutableRefsTable(
       val copiedMap = getOneToManyMutableMap(connectionId)
 
       // Check if the reference already exists. This is needed to make fewer operations and not to break children ordering
-      if (copiedMap.get(childId.arrayId) == parentId.id.arrayId) return emptyList()
+      val existingParent = copiedMap.get(childId.arrayId)
+      if (existingParent != NonNegativeIntIntBiMap.DEFAULT_RETURN_VALUE && existingParent == parentId.id.arrayId) return emptyList()
 
       val removedParent = copiedMap.removeKey(childId.arrayId)
       val removedChildren = copiedMap.putAll(intArrayOf(childId.arrayId), parentId.id.arrayId)
diff --git a/platform/workspace/storage/src/com/intellij/platform/workspace/storage/impl/containers/NonNegativeIntIntBiMap.kt b/platform/workspace/storage/src/com/intellij/platform/workspace/storage/impl/containers/NonNegativeIntIntBiMap.kt
index dcc715d87470..d6887b6d7ac2 100644
--- a/platform/workspace/storage/src/com/intellij/platform/workspace/storage/impl/containers/NonNegativeIntIntBiMap.kt
+++ b/platform/workspace/storage/src/com/intellij/platform/workspace/storage/impl/containers/NonNegativeIntIntBiMap.kt
@@ -110,7 +110,7 @@ internal sealed class NonNegativeIntIntBiMap {
     get() = key2Value.keys
 
   inline fun forEachKey(crossinline action: (Int, Int) -> Unit) {
-    Int2IntMaps.fastForEach(`access$key2Value`, Consumer { action(it.intKey, it.intValue) })
+    Int2IntMaps.fastForEach(key2Value, Consumer { action(it.intKey, it.intValue) })
   }
 
   fun containsKey(key: Int) = key2Value.containsKey(key)
@@ -139,10 +139,9 @@ internal sealed class NonNegativeIntIntBiMap {
     return result
   }
 
-  @Suppress("PropertyName")
-  @PublishedApi
-  internal val `access$key2Value`: Int2IntMap
-    get() = key2Value
+  internal fun assertConsistency() {
+    assert(key2Value.defaultReturnValue() == DEFAULT_RETURN_VALUE)
+  }
 
   companion object {
     internal const val DEFAULT_RETURN_VALUE = -1
diff --git a/platform/workspace/storage/src/com/intellij/platform/workspace/storage/impl/serialization/registration/StorageRegistrar.kt b/platform/workspace/storage/src/com/intellij/platform/workspace/storage/impl/serialization/registration/StorageRegistrar.kt
index eb8ce92028f2..a99175b1b678 100644
--- a/platform/workspace/storage/src/com/intellij/platform/workspace/storage/impl/serialization/registration/StorageRegistrar.kt
+++ b/platform/workspace/storage/src/com/intellij/platform/workspace/storage/impl/serialization/registration/StorageRegistrar.kt
@@ -147,7 +147,12 @@ internal class StorageClassesRegistrar(
     kryo.register(HashBiMap::class.java).instantiator = ObjectInstantiator { HashBiMap.create<Any, Any>() }
     kryo.register(LinkedHashSet::class.java).instantiator = ObjectInstantiator { LinkedHashSet<Any>() }
     kryo.register(LinkedBidirectionalMap::class.java).instantiator = ObjectInstantiator { LinkedBidirectionalMap<Any, Any>() }
-    kryo.register(Int2IntOpenHashMap::class.java).instantiator = ObjectInstantiator { Int2IntOpenHashMap() }
+    kryo.register(Int2IntOpenHashMap::class.java).instantiator = ObjectInstantiator {
+      // We set -1 as a default return value because it's used in all Int2IntOpenHashMap in WM. But it would be better
+      //   to wrap "Int2IntOpenHashMap with default -1" with some helper class to avoid possible issues
+      //   if in some place we'll use this map with different default return value
+      Int2IntOpenHashMap().also { it.defaultReturnValue(-1) }
+    }
     @Suppress("SSBasedInspection")
     kryo.register(ObjectOpenHashSet::class.java).instantiator = ObjectInstantiator { ObjectOpenHashSet<Any>() }
     @Suppress("SSBasedInspection")