diff --git a/platform/lang-impl/src/com/intellij/util/indexing/FileBasedIndexDataInitialization.java b/platform/lang-impl/src/com/intellij/util/indexing/FileBasedIndexDataInitialization.java
index ce0ec195dcef..544ed13bae42 100644
--- a/platform/lang-impl/src/com/intellij/util/indexing/FileBasedIndexDataInitialization.java
+++ b/platform/lang-impl/src/com/intellij/util/indexing/FileBasedIndexDataInitialization.java
@@ -153,12 +153,10 @@ class FileBasedIndexDataInitialization extends IndexDataInitializer<IndexConfigu
         }
       }
 
-      //StaleIndexesChecker.clearStaleIndexes(myStaleIds);
-
       return myState;
     }
     finally {
-
+      myFileBasedIndex.addStaleIds(myStaleIds);
       myFileBasedIndex.setUpFlusher();
       myRegisteredIndexes.ensureLoadedIndexesUpToDate();
       myRegisteredIndexes.markInitialized();  // this will ensure that all changes to component's state will be visible to other threads
diff --git a/platform/lang-impl/src/com/intellij/util/indexing/FileBasedIndexImpl.java b/platform/lang-impl/src/com/intellij/util/indexing/FileBasedIndexImpl.java
index 575800147b16..3f2e04228b5e 100644
--- a/platform/lang-impl/src/com/intellij/util/indexing/FileBasedIndexImpl.java
+++ b/platform/lang-impl/src/com/intellij/util/indexing/FileBasedIndexImpl.java
@@ -60,9 +60,7 @@ import com.intellij.util.indexing.snapshot.SnapshotHashEnumeratorService;
 import com.intellij.util.indexing.snapshot.SnapshotInputMappings;
 import com.intellij.util.io.storage.HeavyProcessLatch;
 import com.intellij.util.messages.SimpleMessageBusConnection;
-import it.unimi.dsi.fastutil.ints.IntArrayList;
-import it.unimi.dsi.fastutil.ints.IntList;
-import it.unimi.dsi.fastutil.ints.IntSet;
+import it.unimi.dsi.fastutil.ints.*;
 import org.jetbrains.annotations.ApiStatus;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
@@ -117,6 +115,7 @@ public final class FileBasedIndexImpl extends FileBasedIndexEx {
   private final AtomicInteger myLocalModCount = new AtomicInteger();
   private final AtomicInteger myFilesModCount = new AtomicInteger();
   private final Set<Project> myProjectsBeingUpdated = ContainerUtil.newConcurrentSet();
+  private final IntSet myStaleIds = new IntOpenHashSet();
 
   private final Lock myReadLock;
   public final Lock myWriteLock;
@@ -310,6 +309,12 @@ public final class FileBasedIndexImpl extends FileBasedIndexEx {
     }
   }
 
+  void addStaleIds(@NotNull IntSet staleIds) {
+    synchronized (myStaleIds) {
+      myStaleIds.addAll(staleIds);
+    }
+  }
+
   static class MyShutDownTask implements Runnable {
     @Override
     public void run() {
@@ -748,11 +753,28 @@ public final class FileBasedIndexImpl extends FileBasedIndexEx {
   }
 
   void filesUpdateStarted(Project project) {
+    ensureStaleIdsDeleted();
     getChangedFilesCollector().ensureUpToDate();
     myProjectsBeingUpdated.add(project);
     incrementFilesModCount();
   }
 
+  void ensureStaleIdsDeleted() {
+    waitUntilIndicesAreInitialized();
+    synchronized (myStaleIds) {
+      if (myStaleIds.isEmpty()) return;
+      try {
+        StaleIndexesChecker.clearStaleIndexes(myStaleIds);
+      }
+      catch (Exception e) {
+        LOG.error(e);
+      }
+      finally {
+        myStaleIds.clear();
+      }
+    }
+  }
+
   void filesUpdateFinished(@NotNull Project project) {
     myProjectsBeingUpdated.remove(project);
     incrementFilesModCount();
diff --git a/platform/lang-impl/src/com/intellij/util/indexing/RegisteredIndexes.java b/platform/lang-impl/src/com/intellij/util/indexing/RegisteredIndexes.java
index c283be3dd21e..d07675e52fdd 100644
--- a/platform/lang-impl/src/com/intellij/util/indexing/RegisteredIndexes.java
+++ b/platform/lang-impl/src/com/intellij/util/indexing/RegisteredIndexes.java
@@ -104,6 +104,7 @@ public final class RegisteredIndexes {
   void ensureLoadedIndexesUpToDate() {
     myAllIndicesInitializedFuture = IndexDataInitializer.submitGenesisTask(() -> {
       if (!myShutdownPerformed.get()) {
+        myFileBasedIndex.ensureStaleIdsDeleted();
         myFileBasedIndex.getChangedFilesCollector().ensureUpToDateAsync();
       }
       return null;