One Drive missing files and folders on both PC app and Online Backup after factory reset

Because relinking already synchronized the same cloud state, recover the files through the OneDrive website now—first from its Recycle Bin, and, if they are absent and you have Microsoft 365, by rolling back OneDrive to a point before the PC failure.

1. Check the OneDrive Recycle Bin

1. Sign in to the OneDrive website with the same Microsoft account used before the reinstall.
2. Select Recycle bin in the left navigation.
3. Look for the missing files and folders.
   • If Personal Vault was involved, select Show Personal Vault items.
4. Select the items and choose Restore.

For a personal account, deleted items can normally be restored for 30 days unless they were permanently removed from the Recycle Bin. Items permanently deleted from that bin cannot be recovered through OneDrive. ^1^

2. Roll back the entire OneDrive

If the Recycle Bin does not contain the files and the loss occurred only a few days ago, use Restore your OneDrive. This requires a Microsoft 365 subscription and can undo deletion, overwrite, or corruption activity from the last 30 days. ^2^

Before proceeding, copy any important files created since the reinstall to a location outside OneDrive.

1. Open the OneDrive website.
2. For a personal account, select Settings → Options → Restore your OneDrive.
3. Select Custom date and time.
4. Choose a point immediately before the Windows failure or reinstall.
5. Review the activity chart and feed for deletions, moves, or other bulk changes.
6. Select Restore.
7. Afterward, verify the affected folders on the website before checking the PC.

This rolls back all selected OneDrive activity, not only the affected folders. Files created after the chosen restore point are moved to the OneDrive Recycle Bin and can be restored separately. If necessary, the rollback itself can be undone by running Restore again and selecting the restore operation.

3. If no cloud recovery contains the files

The factory reset or clean installation does not itself prove that every local file had completed uploading. An empty folder visible both online and on the PC means the PC is now reproducing the cloud state; another unlink/relink will not recreate missing content.

Also check whether the files were stored under another personal, work, or school Microsoft account. Sign into each relevant account through the OneDrive website and search using filenames, file types, dates, and folder names.

If the files never reached OneDrive, recovery is limited to a separate pre-existing backup:

• File History: Connect the external drive or network location previously used for File History, open Control Panel → File History, and restore an earlier version. File History only helps if it was enabled before the failure and its backup survived separately. ^3^
• Other devices: Check any phone, tablet, or second computer that may still hold an offline copy. Disconnect it from the network before opening OneDrive so that synchronization cannot modify that copy.
• External/manual backups: Search any USB drive, NAS, or other backup destination used before reinstalling Windows.

A Windows.old recovery path does not apply to a fresh Windows installation from USB that formatted the drive; Microsoft states that such an installation removes the drive contents. ^4^

If the files are absent from the website search, Recycle Bin, rollback history, every other Microsoft account, and all separate backups, OneDrive cannot restore content that was never uploaded or was permanently removed from its Recycle Bin.

References

1. Restore files deleted from your OneDrive | Microsoft Support
2. Restore your OneDrive | Microsoft Support
3. Backup and restore with File History | Microsoft Support
4. Retrieve files from the Windows.old folder after a Windows upgrade | Microsoft Support