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MicrosoftBecause of the performance benefits and access across devices, we generally recommend that you use folder shortcuts. However, there are a few scenarios for which shortcuts are not yet adequate such as cross-tenant and on-premises.
You can hide the “Sync” button with a cmdlet. Existing relationships are unaffected.
Because of the undeclared desyncing of other content in the directory tree and orphaning of previously synchronised content I am unable to recommend Folder Shortcuts to any organisation with existing Syncs use.
It's an unforgivable mess
https://noviaworks.co.uk/2025/10/09/shortcuts-vs-sync-in-sharepoint-what-really-happens/
I also have serious reservations about mixing shared corporate content in the space+OneDrive) previously used distinctly for personal corporate content.
The 'few' scenarios you mentioned are complete showstoppers for EVERY organisation I work with.