diff --git a/jps/jps-builders/src/org/jetbrains/jps/incremental/storage/TimestampStorage.java b/jps/jps-builders/src/org/jetbrains/jps/incremental/storage/TimestampStorage.java
index be8c788cc25c..49761fe47a36 100644
--- a/jps/jps-builders/src/org/jetbrains/jps/incremental/storage/TimestampStorage.java
+++ b/jps/jps-builders/src/org/jetbrains/jps/incremental/storage/TimestampStorage.java
@@ -78,7 +78,8 @@ public class TimestampStorage extends AbstractStateStorage<File, TimestampStorag
             remove(file);
           }
           else {
-            ArrayUtil.remove(state, i);
+            TimestampPerTarget[] newState = ArrayUtil.remove(state, i);
+            update(file, newState);
             break;
           }
         }