Group policy files deleted manually from the cli are resynced from other servers whenever the group policy sync is triggered.
To avoid this, the sysvol-sync script could lookup to be sync'ed GPOs in the local Samba directory service and exclude unreferenced ones from the merge. The solution needs to consider the special UCS@school case where sync may run on a Master without a local Samba directory service.
Does it happen often?
Every time you try to delete group policy directories/files manually.
We had the error in two cases. UCS with multiple slaves but no Samba 4 on the master and UCS@School with no Samba 4 on the master. I think the error happened every time a policy was deleted using the GPO editior, the file was synced from the master, deleting the policy manually from the master resulted it being synced back from the slaves/backups. I do not think this is currently still relevant, at least neither customer has reported any related issues with UCS 4.1. As UCS 4.0 is out of Maintenance I would close this Bug with Works for me.