I too saw the 99%, it paused a moment, the AC rebooted, the I saw a quick notice, something else was being updated. This took only a couple of seconds, then there was a beep that seemed to come from the controller. It then reboot and completed the update. I could swear the message said programming battery or setting like that.
The other thing, during the AC update, the contoller light blinked furiously until the update was complete. Then it wanted to update the controller, after disconnecting AC and connecting the controller to the tablet, it began updating, when i clicked the update button with the AC still on of course.
Afterwards all seems fine.
BQ