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Dear Mark,
Good day!!
As per the description shared, I understand your concern and to my knowledge, when we remove the shortcuts of the folders in the SharePoint Online site document libraries to the OneDrive for Business, the shortcuts which are synced to the device should be disappeared from the OneDrive synced folder.
Since you have mentioned removing the shortcut from the OneDrive for Business doesn’t remove the shortcut from the OneDrive synced folder, I would like to suggest you try resetting the OneDrive sync client on the problematic user device and check the outcome: Reset OneDrive - Microsoft Support
If still the same problem happens, I would like to request you to remove all the shortcuts added to the user OneDrive for Business via browser and then re-setup the OneDrive account on the user problematic device:
Step 1: Remove the shortcuts added on the user OneDrive for Business (Open the OneDrive for Business in the browser> Right-click on the shortcut and click on Remove Shortcut).
Step 2: Click on the OneDrive icon on the Windows taskbar> Click on the Help & Settings> Settings> Account> Stop sync and unlink this PC.
Step 3: Open the File Explorer> C drive> Users> Folder with the user profile having the problem> AppData> Local> OneDrive> Move the Cache folder to Desktop> Go back to Local folder path> Go to Microsoft folder> OneDrive> Move the complete folders to Desktop location.
Step 4: Restart the device> Setup the user account on the OneDrive sync client again but make sure to choose new location instead of selecting Use this folder.
Moreover, I have done some search where we can only disable Add Shortcut to OneDrive feature on the complete tenant using the PowerShell command: Set-SPOTenant -DisableAddShortCutsToOneDrive $True
Appreciate your patience and understanding. Have a great day!!
Best Regards,
Sophia