Late reply but hopefully someone else already found a fix for it. No matter if I leave the internal AP enabled and have the onion connected over wifi, if an update is performed I have to serial into the device and reconfigure the wifi to get it to connect to my network again.
Was hoping that if the internal AP was left enabled even if the defaults for wifi changed I could VNC into a machine at home and connect to the AP, reconfigure and be back in business. No such luck. Ran the update over VPN and lost all communication. Will have to wait until back home to get it up again.
This should be corrected as if the onion was in a remote embedded project box we should still be able to connect, upgrade, and resume use seamlessly.