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Dear Gila,
Please check whether you encounter the error message like “You’re already syncing a shortcut from this library”. If yes, the possible root cause may be that you add a shortcut of the folder from other sources like the SharePoint Online site library by clicking on Add shortcut to OneDrive. If you sync the folders from the original source again, the error message may pop up.
If yes, you may go to the OneDrive for Business site (https://contoso-my.sharepoint.com/personal/username\_contoso\_onmicrosoft\_com) and check whether there are some shortcut. If yes, remove it and reset OneDrive via the steps in Reset OneDrive - Microsoft Support and then sync the folders from the site library to see the result.
Thanks for your effort and time.
Sincerely
Cliff | Microsoft Community Moderator