diff --git a/services/history-v1/storage/scripts/back_fill_file_hash.mjs b/services/history-v1/storage/scripts/back_fill_file_hash.mjs
index c1d76a8bcd..859c286eb5 100644
--- a/services/history-v1/storage/scripts/back_fill_file_hash.mjs
+++ b/services/history-v1/storage/scripts/back_fill_file_hash.mjs
@@ -676,17 +676,19 @@ async function updateFileRefInMongo(entry) {
  * @param {ProjectContext} ctx
  * @param {Folder} folder
  * @param {string} path
+ * @param {boolean} isInputLoop
  * @return Generator<QueueEntry>
  */
-function* findFiles(ctx, folder, path) {
+function* findFiles(ctx, folder, path, isInputLoop = false) {
   let i = 0
   for (const child of folder.folders) {
-    yield* findFiles(ctx, child, `${path}.folders.${i}`)
+    yield* findFiles(ctx, child, `${path}.folders.${i}`, isInputLoop)
     i++
   }
   i = 0
   for (const fileRef of folder.fileRefs) {
     if (!fileRef.hash) {
+      if (isInputLoop) ctx.remainingQueueEntries++
       yield {
         ctx,
         cacheKey: fileRef._id.toString(),
@@ -725,12 +727,14 @@ function* findFileInBatch(
       projectBlobs,
       projectBackedUpBlobs
     )
-    yield* findFiles(ctx, project.rootFolder[0], prefix)
+    yield* findFiles(ctx, project.rootFolder[0], prefix, true)
     for (const fileId of projectDeletedFiles) {
+      ctx.remainingQueueEntries++
       yield { ctx, cacheKey: fileId, fileId, path: '' }
     }
     for (const blob of projectBlobs) {
       if (projectBackedUpBlobs.has(blob.getHash())) continue
+      ctx.remainingQueueEntries++
       yield {
         ctx,
         cacheKey: blob.getHash(),
@@ -821,6 +825,9 @@ class ProjectContext {
   /** @type {Set<string>} */
   #historyBlobs
 
+  /** @type {number} */
+  remainingQueueEntries = 0
+
   /**
    * @param {ObjectId} projectId
    * @param {string} historyId
@@ -877,6 +884,10 @@ class ProjectContext {
   }
 
   async flushMongoQueuesIfNeeded() {
+    if (this.remainingQueueEntries === 0) {
+      await this.flushMongoQueues()
+    }
+
     if (this.#completedBlobs.size > BATCH_HASH_WRITES) {
       await this.#storeBackedUpBlobs()
     }
@@ -1022,7 +1033,11 @@ class ProjectContext {
     } else {
       this.#pendingFiles.set(entry.cacheKey, processFileWithCleanup(entry))
     }
-    entry.hash = await this.#pendingFiles.get(entry.cacheKey)
+    try {
+      entry.hash = await this.#pendingFiles.get(entry.cacheKey)
+    } finally {
+      this.remainingQueueEntries--
+    }
     this.queueFileForWritingHash(entry)
     await this.flushMongoQueuesIfNeeded()
   }