I ran down my 12V battery once and after letting the car sit for a few hours, it was able to start whereas before, all attempts failed. I think the 12V battery might have charged up a little from the traction battery.

Otherwise, I would've gotten a car battery charger, disconnected the 12V battery from the car and trickle charged it. On page 294 of the manual, there's a special procedure for starting up after recharging the battery.