Especially if is using the python gpio library and resetting the state in some way.
We can mark this solved. I would if I knew how.
I made a blunder in my sending signals to a python process from the node-red flow and was stopping everything python, but not python3 which is what made me miss diagnose it I was using Thonny over ssh -X for the python code development and it continued to work which pointed me to the a node-red problem instead of a python problem.