Assuming I'm following correctly, I'm not seeing the same behaviour.
- Drop a debug node into the flow and deploy.
- Edit the debug node and turn off Enabled - blue dot appears and Deploy turns red.
- Go to another flow and ctrl-Z - Deploy reverts to grey.
- Go back to initial flow and the blue dot is gone. This is where you're still seeing the blue dot?
However, I came here to see if something else has been reported as a bug with undo:
- Link 3 nodes
- Delete the middle node
- ctrl-Z to undo
- The middle node comes back, but the links do not. This is with NR 2.2.2, but I reckon it has been around for a while.