I just had this happen too and both of my control units are essentially unusable stuck at "NOW UPDATING" in part two (USB stick #2) of the upgrade process. They have been sitting here for over an hour, and the timer is not increasing. My NMEA 2000 network is very small and everything else is powered off.
I was upgrading because one of the control units had older software than the other (a newer unit). I've already sent a note into support, but is there a way to reset the control units to try things over again?