Although I don't have a pi3b+ I'm trying to see if I can reproduce your issue on my old Pi2 running same OS version.
Not found any issues yet
I tried again today with full deploy and got it to happen again, but retrying with only deploying modified nodes it seems to no longer happen. Even when the modified nodes are one or both of the GPIO nodes, their functionality now appears unaffected.
The OS itself did still see the GPIO inputs behaving correctly even when the GPIO nodes did not.
So from this it is apparent that whatever it is that causes the issue is common to both node-red-node-pi-gpio and node-red-node-pi-gpiod, and only gets triggered sometimes on full deployment of the flow.
Unrelated to node-red I have also been experiencing a problem with the RPi hanging on shutdown or reboot, which seems to be a problem caused by a service associated with the Waveshare 5 inch 800x400 HDMI LCD connected to the Pi. It is connected to the GPIO header, intended to send resistive touch screen data over it using SPI however I never got that to work. The pins I am using for node red input are not ones used by the display and are just physically passed through, but at this point I feel like this may as well be part of the problem because it's the only major difference I can see between my RPi and anyone else's trying to replicate the issue.
