I think I had something similar the other week when sync wasnt working, i changed some IP addresses in NPM (50) and the two db's got out of sync. When you run the db sync it then copies the old nodes (old IP addresses) back into NPM, however the new CoreID in NCM is different to the NPM NodeID as it created new nodes.
it was a mixture of updating IPs on NCM, then updating CoreNodeID, but i was working on an active support call at the time.