Index: src/main/java/org/apache/jackrabbit/oak/plugins/backup/FileStoreBackup.java
===================================================================
--- src/main/java/org/apache/jackrabbit/oak/plugins/backup/FileStoreBackup.java	(revision 1656785)
+++ src/main/java/org/apache/jackrabbit/oak/plugins/backup/FileStoreBackup.java	(working copy)
@@ -77,7 +77,7 @@
                 }
             }
 
-            Compactor compactor = new Compactor(backup.getTracker().getWriter());
+            Compactor compactor = new Compactor(backup.getTracker().getWriter(), true);
             SegmentNodeState after = compactor.compact(before, current);
 
             // 4. commit the backup