A mention of note, all the 'bad' monitors I've unmanaged through the node, so they aren't causing issues at the moment, but how can I go from the specific app no longer being managed to being deleted?
After getting on the phone with support, I had enough backup to try the fix I was thinking of. So here is the fix...
On the bad application scanner assigned to a node, go into that node and then go into that application scanner.
Edit that application scanner from within the node.
Rename that application scanner to indicate it is a bad check. I renamed mine to ...-Bad One.
Go into the application assignments list.
Find the newly renamed bad scanner and delete it.
The bad scanner is now gone!