Lipo at 2.6V?

I purchased 2 zippy 3S, 20-30C, 5000mah lipos and have been running them in my e-revo. One pack was perfectly balanced, the other had one cell about half a volt lower than the other two. I have a charger that balances the lipos and when I'd charge them, I'd plug in the balancer (thinking it was supposed to balance). Today, I was running the car and I noticed the power seemed like it wasn't there. I was expecting that MM to kill the power but it never did. I brought it in, held the wing and gave it a few throttle pulls. Never turned off. I pulled the batteries and went to charge them. The one cell was at 2.6v. Within 30 seconds it powered up to 3.1V and the other two cells were at 3.6v. I found out last night that in order to balance, I had to use the balance part of the charger. I did this next and they were balanced in 15 minutes.

Question #1: Did I harm the battery? It doesn't appear that I did. There is no swelling and it wasn't any warmer than typical.

Question #2: Why didn't the ESC kill the power? My guess, it's on Auto Lipo. The ESC thought it was a 5S and not a 6S "thinking" there was more power to use. Lesson, turn off auto lipo?

Thanks in advance.