Issue
When a target mailbox is provisioned and synced, certain folders that are considered system folders are not created during the initial provisioning but can be taken over by the system once the mailbox is logged into.
In this case, the "Clutter" folder was copied from the source to the target and when the Target mailbox was accessed the Clutter folder was marked as a special system folder, protecting it from a deletion. The Sync had copied the folder so a special property was placed on the folder to indicate that P365 had synced it (this is the property that allows us to rollback items and folders that have been synced).
There was some alteration to the folder in the source to the point that the sync wanted to remove it and recreate it. The reason it concluded it could remove it was that it is empty in the target.
Solution
We have a script that can log into a mailbox using Exchange Web Services and remove the properties on the folder that identify it as synced by P365.
After this process the sync should simply match it as a pre-existing folder and merge the content into it.
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