diff --git a/opengrok-indexer/src/main/java/org/opengrok/indexer/index/IndexDatabase.java b/opengrok-indexer/src/main/java/org/opengrok/indexer/index/IndexDatabase.java
index 5ff11bbc0b2..de89aa00b81 100644
--- a/opengrok-indexer/src/main/java/org/opengrok/indexer/index/IndexDatabase.java
+++ b/opengrok-indexer/src/main/java/org/opengrok/indexer/index/IndexDatabase.java
@@ -1798,9 +1798,8 @@ void processFileHistoryBased(IndexDownArgs args, File file, String path) throws
                 boolean matchOK = (isWithDirectoryCounts || isCountingDeltas) &&
                         checkSettings(termFile, termPath);
                 if (!matchOK) {
-                    removeFile(false);
-                    addWorkHistoryBased(args, termFile, termPath);
                     deletedUidsHere.add(removeFile(false));
+                    addWorkHistoryBased(args, termFile, termPath);
                 }
             } else {
                 deletedUidsHere.add(removeFile(!fileExists));