Yeah, we had that problem when we moved over to v10. But now we do DB Sync's to bring back all the missed nodes to be able to remove them from NCM.
This is my arguement for bringing the Console Back...I would prefer to be able to add/remove nodes from either NPM or NCM as I choose... instead of having to remove NCM first and then do a DB sync. With the sync's it keeps our DB's matching.