diff --git a/jps/jps-builders/src/org/jetbrains/jps/incremental/storage/BuildTargetConfiguration.java b/jps/jps-builders/src/org/jetbrains/jps/incremental/storage/BuildTargetConfiguration.java
index b52c8c6a7666..0a60b075d21d 100644
--- a/jps/jps-builders/src/org/jetbrains/jps/incremental/storage/BuildTargetConfiguration.java
+++ b/jps/jps-builders/src/org/jetbrains/jps/incremental/storage/BuildTargetConfiguration.java
@@ -185,7 +185,7 @@ public class BuildTargetConfiguration {
           }
         }
         if (wasDeleted) {
-          nonexistentOutputRoots.add(outputRoot.getAbsolutePath());
+          nonexistentOutputRoots.add(FileUtil.toSystemIndependentName(outputRoot.getAbsolutePath()));
         }
       }
     }