Short Update here:
The affected systems seem to fetch one of the UIDs from another system and kick that one out of the ePO.
After the other systems report back in to the ePO the probelmatic systems get completely removed from ePO.
I created a service ticket with McAfee
Just for the case that someone has the same problems.
In our case all this behaviour was caused because the clients were connecting via VPN an as such had all the same MAC-Adresses.
This in combination with the AD-Sync task caused duplicates on the one site and the deletion of others systems connectin also via VPN on the other side.
The solution was to stick to the following KB: