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.

I believe Benjamin is correct. Those sentences are in fact NMEA compliant and indicate no fix yet. Received my receiver from onion.io last week and it took about 20 minutes outside for TTFF and went full 3D. After than cold restarts using u-center it only took seconds to hit 2D fix.

You may be able to speed it up by using u-center's AssistNow and push the almanac manually.