OneDrive for Business file server migration troubleshooting for mergers: misses files

During a merger, you need to migrate file server data to OneDrive for Business. When the migration completes, some files are missing. This happens because of permission mismatches, file name length limits, or blocked file types. This article explains why files get skipped during migration and how to find and fix the missing items.

Why File Server Migrations Miss Files During Mergers

When you migrate files from an on-premises file server to OneDrive for Business, the Microsoft 365 Migration API or third-party tools copy files based on source permissions. If a user or group in the source Access Control List no longer exists in the target tenant, the file is skipped. This is common in mergers because the acquiring company’s tenant may not have the acquired company’s user accounts or security groups yet.

Another cause is file name and path length. OneDrive for Business supports paths up to 400 characters. Any file with a longer path is silently skipped during migration. Also, OneDrive blocks specific file types, such as executable files (.exe, .msi) and script files (.vbs, .ps1). If your file server stored these types, they will not be migrated.

A third cause is sync conflicts. If a file is open on a user’s device during the migration window, the migration tool may skip it to avoid corruption. The file appears in the skipped items log but is not copied to OneDrive.

Steps to Locate and Migrate Missing Files

Follow these steps to find which files were skipped and then migrate them manually or with a targeted retry.

1. Open the Migration Dashboard in Microsoft 365 Admin Center
   Go to Admin centers > Migration. Select the completed migration batch. Click View details to open the summary page.
2. Download the Failed Items Report
   On the summary page, click Download failed items report. This CSV file lists every file that was not migrated, along with a reason code such as PathTooLong, FileTypeBlocked, or AccessDenied.
3. Fix Permission Mismatches for Access Denied Errors
   For each file with AccessDenied, check the source file server’s NTFS permissions. Ensure the target user or group exists in the Microsoft 365 tenant. If the group is missing, create it in Azure Active Directory > Groups and add the user. Then retry the migration for that file only.
4. Shorten Paths for PathTooLong Errors
   Files with PathTooLong have a full path over 400 characters. On the source file server, rename deeply nested folders or move the file to a shallower folder. After the change, run a delta migration for the affected folder only.
5. Unblock or Rename Blocked File Types
   Go to OneDrive admin center > Sync > File types. Review the list of blocked extensions. If you need to migrate .exe or .vbs files, remove the extension from the block list, or rename the files to a safe extension like .exe.old before migration.
6. Retry the Migration for the Specific Folder or User
   In the Migration dashboard, select the affected user or folder. Click Retry. The migration tool will copy only the files that previously failed.

When Files Are Still Missing After Retry

OneDrive Sync Client Shows Files as Not Synced

After migration, the OneDrive sync client may show a red X or a sync pending icon on some files. This usually means the file is still open on the source server. Close the file on the server, then right-click the OneDrive icon in the system tray and select Resume syncing. If the file still does not sync, check the sync client’s activity center for the exact error.

Files Are in the Source but Not in OneDrive and Not in the Report

If a file is missing from OneDrive and does not appear in the failed items report, the migration tool may have skipped it silently due to a temporary network issue. Run a manual delta migration for the entire parent folder. In the Migration dashboard, select the user’s migration, click Edit, and enable Delta migration. Set the delta window to cover the original migration date.

Files Are Present but Cannot Be Opened

Some files may migrate but become corrupted due to a partial transfer. The failed items report will show IncompleteTransfer. Delete the corrupted file from OneDrive, then retry the migration for that specific file using the Retry button in the dashboard.

File Server vs OneDrive for Business: Key Differences for Migration

Item	File Server	OneDrive for Business
Path length limit	32,767 characters (NTFS)	400 characters
Blocked file types	None by default	Executables, scripts, system files blocked
Permission model	NTFS ACLs with local or domain groups	Azure AD groups and user accounts
Open file handling	File can be locked by a user	Skipped during migration if open

Now you can locate every missing file using the failed items report and fix the root cause for each error code. Before starting a new migration batch, shorten folder paths to under 400 characters and verify that all source security groups exist in Azure AD. For ongoing sync health, enable the OneDrive sync client’s Files On-Demand setting to avoid local disk space issues on user devices.