OneDrive Admin Checklist: file server migration misses files for finance folders

When migrating files from a legacy file server to OneDrive, finance folders are often the most complex to transfer. These folders typically contain deeply nested subfolders, long file paths, and many files with restricted permissions. A migration that completes without errors can still leave dozens or hundreds of files behind, especially in finance directories. This article explains why finance folders are prone to missing files during migration and provides a step-by-step checklist to verify and fix the transfer.

Why Finance Folder Migrations Leave Files Behind

Finance folders on file servers often accumulate files over many years. Accountants and auditors store historical data in deep folder hierarchies such as Finance\2024\Q4\Audit\WorkingPapers\Draft\Version3. These paths can exceed OneDrive’s 400-character limit, causing the migration tool to skip the file silently. The SharePoint Migration Tool (SPMT) does flag these files in its scan report, but many administrators only check the final migration summary, which shows the file count as “completed” even when individual files are omitted.

A second common cause is file locking. Finance teams frequently work on Excel workbooks and PDFs that are opened by multiple users. If a file is open on a user’s workstation during the migration window, SPMT cannot copy it. The tool logs this as a “file in use” error, but the file is not automatically retried. The migration report may show a warning, but busy administrators can miss it.

Permission inheritance is another factor. Finance folders often have custom NTFS permissions that break inheritance at the subfolder level. SPMT can map these permissions to SharePoint, but if the target OneDrive library has restrictive sharing settings, the migration may skip folders that cannot inherit the parent’s permissions. This results in empty folders in OneDrive with no visible error.

Checklist to Verify and Complete the Migration of Finance Folders

Use this checklist after the SPMT migration job finishes. Each step addresses a specific failure pattern found in finance folder transfers.

Step 1: Run SPMT Scan Report on Finance Folders Before Migration

1. Open SharePoint Migration Tool
   Launch SPMT from the Microsoft 365 admin center or download it from the Microsoft 365 apps page. Sign in with a Global Admin or SharePoint Admin account.
2. Select the finance folder source
   Choose File share as the source type. Enter the UNC path to the top-level finance folder, for example \\fileserver\share\Finance.
3. Run a scan only
   In the SPMT wizard, select Scan only instead of Scan and migrate. SPMT will analyze the folder structure and produce a CSV report of all files and any issues.
4. Review the scan report
   Open the generated CSV file. Filter the Issue column for values such as Path too long, File in use, File name contains invalid characters, and Permission issue. Note every file that has a problem.

Step 2: Fix Path Length Violations

1. Identify files with paths over 400 characters
   In the scan report CSV, filter for Path too long. Copy the full file path for each flagged file.
2. Shorten the folder structure on the file server
   Move files from deep subfolders to a shallower location. For example, move Finance\2024\Q4\Audit\WorkingPapers\Draft\Version3 to Finance\2024-Q4-Audit. Use a rename or move operation on the file server before re-running the migration.
3. Re-run SPMT scan
   After restructuring, run another scan-only pass to confirm no path length issues remain.

Step 3: Handle Files Locked by Users

1. Check the scan report for locked files
   Filter the Issue column for File in use or Locked by.
2. Notify users to close files
   Send an email to finance staff asking them to close all Excel workbooks, PDFs, and other documents in the shared folder. Schedule the migration run during a time when finance users are not working, such as overnight or on weekends.
3. Use SPMT retry option
   In SPMT, after the first migration completes, select Retry failed items. SPMT will attempt to copy only the files that were skipped due to locking.

Step 4: Verify Permission Inheritance and Target Library Settings

1. Check NTFS permissions on the source folder
   On the file server, right-click the finance folder, select Properties, go to the Security tab, and click Advanced. Look for any folder that has Inheritance set to Disabled. Note the folder names.
2. Map folder permissions in SPMT
   In SPMT, under Settings, enable Preserve file share permissions. This tells SPMT to copy NTFS permissions to SharePoint.
3. Check target OneDrive library sharing settings
   In the Microsoft 365 admin center, go to SharePoint > Policies > Sharing. Ensure that Allow sharing to external users is not set to Only people in your organization if finance folders need to be shared with external auditors. If sharing is restricted, folders with custom permissions may fail to migrate.

Step 5: Compare Source and Destination File Counts

1. Count files on the source
   On the file server, open a command prompt and run: dir \\fileserver\share\Finance /s /a:-d | find "File(s)". Note the total file count.
2. Count files in the OneDrive destination
   Open the OneDrive folder in File Explorer. Right-click the finance folder and select Properties. Compare the number of files with the source count.
3. Use PowerShell to compare folder contents
   Run the following PowerShell script to list all files in both locations and export differences to a CSV:
   Get-ChildItem -Path "C:\Users\%username%\OneDrive - Company\Finance" -Recurse -File | Select-Object FullName | Export-Csv -Path "C:\temp\onedrive-files.csv"
   Then compare with the source file list using Compare-Object.

If Files Are Still Missing After the Checklist

OneDrive sync shows a red circle with a white X on finance folders

A red X on a folder icon means OneDrive cannot sync that folder at all. This often occurs when the folder name contains characters that OneDrive does not support, such as #, %, &, or a trailing space. Rename the folder on the file server to remove these characters, then re-run the SPMT migration for that folder only.

Files appear in OneDrive but are empty or corrupt

Zero-byte files in OneDrive indicate that the migration copied the file metadata but not the content. This happens when the source file is encrypted with BitLocker and the migration tool cannot read the decrypted content. Decrypt the file on the source server before migrating, or use the Azure Information Protection scanner to decrypt files before transfer.

Finance subfolders are missing entirely

If a whole subfolder is missing from OneDrive, check the source folder’s permissions. The user account used for migration must have Read and List Folder Contents permissions on every subfolder. If the account lacks access, SPMT skips that subfolder without error. Grant the migration account Full Control on the top-level finance folder temporarily, then re-run the migration.

SPMT Scan vs Full Migration: Key Differences for Finance Folders

Item	Scan Only	Full Migration
Description	Analyzes folder structure and files without copying data	Copies files and permissions to OneDrive or SharePoint
Output	CSV report with file paths, sizes, and issue codes	OneDrive folder with migrated files and permissions
Time required	Minutes to hours depending on file count	Hours to days for large finance folders
Risk of data loss	None — no data is copied	Files may be skipped silently if issues are not pre-scanned
Best use case	Run before migration to identify blocked files	Run after scan shows zero issues

Running a scan-only pass on finance folders before the full migration reduces the chance of missing files by over 90 percent. The scan report acts as a checklist for administrators to fix path lengths, locked files, and permission issues in advance.

After completing the checklist, you can confirm that every finance folder file has been transferred to OneDrive. Use the SPMT retry option for any remaining locked files. For ongoing protection, enable Known Folder Move for finance users so their local Desktop, Documents, and Pictures folders are automatically backed up to OneDrive. Set a retention policy in the Microsoft 365 compliance center to keep finance folder files for seven years.