Hi @Kejnik, Marcin,
It is possible for some folders to be left out of the OneDrive backup when enabling sync, even though they should be moved to the user's OneDrive folder. This can result in unsynced data and is not ideal. One possible solution is to use Configuration Manager to move the Windows known folders to OneDrive for Business. This can be done by creating OneDrive for Business Profiles and specifying settings for moving the Windows known folders, including Desktop, Documents, and Pictures. This can help ensure that all necessary folders are moved to OneDrive and not left out in the user profile.
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