I imported a flow from the store, and there were a couple of missing nodes. I couldn't be bothered to install them as they weren't the ones I was interested in. So, before I DEPLOYed them I deleted them from the editor. On the next DEPLOY NR stopped with the above message.
How is that possible if I didn't deploy them?
Rather than getting the message above, can this scenario be handled with a bit more sympathy, meaning asking if you want to delete them at that point?
Also, when you deployed, you would have got a notification in the deploy popup saying unused configuration nodes. It is worth watching for that when deploying after removing stuff.
If you had used Undo (Ctrl+Z) to undo the import then it would have removed the config nodes also.