I have been using HA for several years, my Pi install is full of testing scenarios, probably not needed in a backup/restore upgrade.
Is there a process/checklist to manually update the Yellow from the Pi, things like moving IKEA Tradfri from an IKEA hub to Zigbee2MQTT come to mind. I appreciate this will mean resetting everything.
My MQTT installation has thousands of devices that my SDR radio has picked up over time, so that integration will have to be rewritten.