When I first got the Prius, I saw my battery drain low very when going through a car wash too. At first, I tried forcing the battery to charge up before going into the carwash. Then I realized it was the A/C that drains the battery so quickly, so I started shutting off the A/C when I get to the carwash. I haven't had the issue since.
Oohhh ok, THANK YOU! I forgot that it's been awhile since I took it in, and was probably in the summer. It's tough here in the summer to go through a car wash & turn your A/C off when it's 115 outside! I'll keep that in mind though when I take it in next time, and make sure the air is completely off!
Why do you think the battery was about to go dead? Just because the anal retentive MFD squawks doesn't mean there is anything -actually- wrong. It's just a warning to not leave it in "N" for long periods of time. Meaning 30 min to an hour. Because it won't charge while in "N", no matter what else you do. Do remember the battery charge state display "zeros out" at 40% battery charge. Make sure the A/C auto is off and the system is not trying to cool the car. Turn off the headlamps. It will be fine for the 1-5 min it takes to go through a car wash. Note that you get the same warning when you open the drivers side door while in "D". So that should tell you it's not really that smart.
I can't remember exactly what it started doing (since it was last summer) - but it seemed like it was more than just the standard message telling you it doesn't charge in Neutral. The dash was lit up like a christmas tree it seemed, and was basically telling me to take it out of neutral. There was 1 little faint pink line at the bottom of the battery on the screen. I bet it was the A/C that did it so fast, like ryogajyc stated. After driving out, I sat in the parking lot to let it charge up, and it took about 5-10 minutes of the engine running to get the battery up enough to where it shut off again. I only lived a few miles down the road, so wanted to get it charged as much as I could before driving home. There was also not much acceleration as I left the car wash.
I remember seeing the blurb about it not charging in Neutral, and I thought, "Oh, didn't know that.. I should be fine." Then when it started screaming at me toward the end of the wash, I was panicking, not sure if I should put it back in drive, and slowly go through the rest of the wash in drive or not. I believe I did shut everything off at that point, but it was already mostly drained.