Fix: Duplicate SharePoint Folders Showing in File Explorer

A customer noticed that the same SharePoint folders were appearing twice in their File Explorer, with both copies showing the same files. They were not sure which one was the “real” folder and were worried about accidentally deleting something. This happens more often than you would think, usually after a SharePoint library is synced more than once or after a change to the sync configuration. The fix is straightforward, but there is a specific order of operations to follow to avoid losing files. Here is how to clean it up safely.

Symptoms

When opening File Explorer, users see two or more copies of the same SharePoint document library or folder:

The same SharePoint folder appears multiple times in File Explorer under the OneDrive section, with identical or near-identical file contents.

• Two or more folders with the same name appear in the left sidebar or under OneDrive - [Your Organisation].
• Both folders contain the same files and appear to sync normally.
• Creating or editing a file in one folder may or may not reflect in the other.
• OneDrive may show sync status icons on both folders.

Duplicates with a “(1)” on the end after a OneDrive reset or relink

A second pattern appears after OneDrive has been reset, unlinked and relinked, or signed in again. Each library shows up twice in File Explorer, one copy with (1) on the end of its name, such as Operations - Projects (1). In OneDrive Settings > Account you may see two entries for your own OneDrive, one saying Not syncing and one showing 0 KB, and libraries that report 0 KB even though the folder holds hundreds of gigabytes. Desktop, Documents and Pictures may also stop working, and a library you expect can be missing completely.

Affected Software

• Application: Microsoft OneDrive for Business (desktop sync client)
• Platform: Windows 10 / Windows 11
• Related Services: SharePoint Online, Microsoft 365

Cause

Duplicate SharePoint folders in File Explorer are typically caused by:

• Syncing the same library more than once, for example by clicking the Sync button in SharePoint when the library was already synced.
• Adding a shortcut and a full sync of the same library. The “Add shortcut to OneDrive” and “Sync” buttons in SharePoint create different types of connections, and using both on the same library will produce duplicates.
• A reset or relink that left the old sync folders behind. When OneDrive is relinked, it finds the old folders still on disk and creates new ones with “(1)” on the end instead of reusing them. If the relink happens in stages (your own OneDrive first, then the team libraries later), the original OneDrive folder can be orphaned. Known Folder Move then keeps pointing Desktop, Documents and Pictures at the orphaned folder, which is why they stop working.
• Leftover sync metadata from a previous sync that was not fully cleaned up, often after a user profile migration, device replacement, or OneDrive reset.

Resolution

Step 1: Stop the Duplicate Sync

1. Click the OneDrive cloud icon in the system tray (bottom right of your screen).
2. Click the gear icon and select Settings.
3. Go to the Account tab.
4. You will see a list of all synced SharePoint libraries. Identify the duplicate entry.
5. Click Stop sync next to the duplicate library.
6. Confirm the warning message when prompted.

Step 2: Delete the Local Folder

Once sync is stopped, the folder will no longer update with SharePoint. You can now safely delete the local folder from File Explorer.

Important: This will not delete the files from SharePoint. It only removes the local copy. As long as you stopped the sync first, your files are safe in SharePoint.

Step 3: Clear OneDrive Sync Cache (if duplicates persist)

If the duplicate folder reappears after deleting it:

1. Close all Office applications.
2. Press Win + R, type %localappdata%\Microsoft\Office\Spw and press Enter.
3. Delete all files and folders in this directory. This clears cached sync data that may be causing the duplication.
4. Restart OneDrive by right-clicking the OneDrive icon in the system tray, selecting Close OneDrive, then reopening it from the Start menu.

Step 4: Re-sync from SharePoint (if needed)

If you need to re-establish the sync connection after cleaning up:

1. Open your browser and navigate to the SharePoint document library.
2. Click the Sync button in the toolbar at the top of the page.
3. A prompt will appear asking for permission to open Microsoft OneDrive. Click Open Microsoft OneDrive.
4. The library will sync and appear in File Explorer under OneDrive - [Your Organisation].

Tip: Using the Sync button from the SharePoint web interface (rather than any local shortcut) is the most reliable way to set up a clean sync connection.

Step 5: If the duplicates appeared after a reset or relink (“(1)” folders)

We fixed this for an engineering firm’s financial controller whose OneDrive had been relinked twice in one afternoon. Every team library was duplicated with “(1)”, one library was missing, and her desktop files had stopped syncing. Stopping sync on the “(1)” copies alone was not enough, because the original folders were orphaned and could hold changes that never reached SharePoint. This is the order that works safely:

1. Back up first. Copy anything that exists only on this PC (Desktop, Documents, Pictures and any files without a green tick or cloud icon) to a folder outside OneDrive, such as C:\Backup\OneDrive. Do not copy cloud-only placeholders, or Windows will try to download the whole library.
2. Close OneDrive completely. If it is stuck part way through adding a library, end OneDrive.exe in Task Manager.
3. Rename the stale folders. Add something like .OLD to the end of the orphaned library folders and the “(1)” copies, so the clean names are free for OneDrive to use again. Keep them until you have checked nothing is missing.
4. Fix Known Folder Move. In OneDrive Settings, go to Sync and backup > Manage back up and make sure Desktop, Documents and Pictures point at your current OneDrive folder. Your IT administrator can also check the paths under HKCU\Software\Microsoft\Windows\CurrentVersion\Explorer\User Shell Folders.
5. Relink once. Open OneDrive Settings, choose Account > Unlink this PC, then sign in again and let your own OneDrive finish setting up before you add anything else.
6. Add each library back once. Open each SharePoint library in your browser and click Sync or Add shortcut to OneDrive. This is also how to bring back a library that is missing from File Explorer even though you can open it on the web.
7. Reconcile the old copies. Compare the .OLD folders with SharePoint. If a file was edited offline and differs from the SharePoint copy, check its Version history in SharePoint before deciding which one to keep. Delete the old folders only when you are sure.

If OneDrive keeps creating “(1)” folders, the PC may have orphaned sync root registrations or a damaged account registration left behind. That needs an administrator to clean up, so contact your IT support rather than resetting OneDrive again.

Verify the Fix

1. Open File Explorer and confirm only one copy of the SharePoint folder appears.
2. Open a file from the folder to confirm it loads correctly.
3. Check the OneDrive icon in the system tray shows a green checkmark (fully synced).

Important Notes

• Always stop the sync before deleting the folder. If you delete a synced folder without stopping the sync first, OneDrive may try to sync that deletion back to SharePoint, potentially removing files for everyone.
• Sync vs. Shortcut: Microsoft recommends using Add shortcut to OneDrive for most users instead of the Sync button. Shortcuts are easier to manage and less prone to duplication issues. Avoid using both methods on the same library.
• Do not reset OneDrive repeatedly. Each reset or relink can create another set of “(1)” folders. Back up and follow Step 5 once instead.
• Check other devices. If the user syncs SharePoint on multiple devices, the same duplicate issue may need to be fixed on each one.
• Intune auto-sync policies: If your organisation uses Intune to auto-sync SharePoint libraries, duplicate folders can appear when policies overlap or when a user also manually syncs a library that is already auto-synced. Check with your IT administrator if duplicates keep reappearing.

Related Resources

• Microsoft Excel cannot access the file on SharePoint
• Microsoft: Sync SharePoint and Teams files with your computer
• Microsoft: Add shortcuts to shared folders in OneDrive
• Microsoft: Back up your folders with OneDrive
• GCIT: Fix “You’re already syncing a shortcut” in OneDrive / SharePoint

If you need help resolving SharePoint sync issues or cleaning up duplicate folders, get in touch with our team.