Hello, thank you for reaching out to Microsoft Q&A.
I understand that your files are missing from your OneDrive folders.
Could you please let me know if you experience the same issue when signing in to your account in the OneDrive web version?
Open an incognito/private browsing window and sign in with your Microsoft account here:
https://onedrive.live.com/
Check whether all the files are available in those folders.
If you can see the files on OneDrive online but not in the OneDrive desktop app, this clearly indicates a sync issue between the app and OneDrive cloud storage.
If that is the case, you can try resetting OneDrive or re-linking your OneDrive account to your Windows device.
-To reset OneDrive, follow the steps here:
Reset OneDrive
-To unlink and re-link OneDrive-
- Right-click the OneDrive icon on the taskbar, select Settings > Accounts > Unlink this PC.
- Sign in with your account again.
If you no longer see the files in Online, check OneDrive and the desktop recycle bin folder. Check whether the files have been moved there. If you see those files, you can restore them to the destination folder.
If you have an Office 365 subscription as well, you can restore OneDrive to earlier versions.
Restore your OneDrive
Let me know if you still need more help.