diff --git a/server/src/main/java/org/elasticsearch/index/store/Store.java b/server/src/main/java/org/elasticsearch/index/store/Store.java
index 7aab2c750d139..666a67de2218b 100644
--- a/server/src/main/java/org/elasticsearch/index/store/Store.java
+++ b/server/src/main/java/org/elasticsearch/index/store/Store.java
@@ -661,17 +661,17 @@ private static void failIfCorrupted(Directory directory, ShardId shardId) throws
     public void cleanupAndVerify(String reason, MetadataSnapshot sourceMetaData) throws IOException {
         metadataLock.writeLock().lock();
         try (Lock writeLock = directory.obtainLock(IndexWriter.WRITE_LOCK_NAME)) {
-            final StoreDirectory dir = directory;
-            for (String existingFile : dir.listAll()) {
+            for (String existingFile : directory.listAll()) {
                 if (Store.isAutogenerated(existingFile) || sourceMetaData.contains(existingFile)) {
                     continue; // don't delete snapshot file, or the checksums file (note, this is extra protection since the Store won't delete checksum)
                 }
                 try {
-                    dir.deleteFile(reason, existingFile);
+                    directory.deleteFile(reason, existingFile);
                     // FNF should not happen since we hold a write lock?
                 } catch (IOException ex) {
                     if (existingFile.startsWith(IndexFileNames.SEGMENTS)
-                            || existingFile.equals(IndexFileNames.OLD_SEGMENTS_GEN)) {
+                            || existingFile.equals(IndexFileNames.OLD_SEGMENTS_GEN)
+                            || existingFile.startsWith(CORRUPTED)) {
                         // TODO do we need to also fail this if we can't delete the pending commit file?
                         // if one of those files can't be deleted we better fail the cleanup otherwise we might leave an old commit point around?
                         throw new IllegalStateException("Can't delete " + existingFile + " - cleanup failed", ex);
@@ -680,6 +680,7 @@ public void cleanupAndVerify(String reason, MetadataSnapshot sourceMetaData) thr
                     // ignore, we don't really care, will get deleted later on
                 }
             }
+            directory.syncMetaData();
             final Store.MetadataSnapshot metadataOrEmpty = getMetadata(null);
             verifyAfterCleanup(sourceMetaData, metadataOrEmpty);
         } finally {