Solved! Go to Solution.
If you perform the unregister on the replica as the replica owner (user) it works cleanly. If you do this as any other user (even as SDE) it may not get deleted entirely, requiring the use of SDE command line to delete sync send versions. That's been my experience at least...
When you unregister a replica, be sure to do it on both ends; you need to 'cut the cord' between parent and child on the parent end and the local/ child end as well.
This poses somewhat of a problem. If an ArcGIS Server administrator is using a Geodata Service to accept data updates from users, the client controls when they make (register) the replica and if/when they choose to unregister it. As the data administrator, one can very quickly end up with many replicas and not know which ones are being used, and/or which ones have been unregistered client-side.
http://ideas.arcgis.com/ideaView?id=087E00000004rvpIAA
For the near-term its probably best to have pretty tight permissions on the ArcGIS Server as to who can access your GeoData services.