If it's an issue with some cells being weak, or out of whack on the balance, running it to zero may seriously push the one bank that is low WAY LOW, ie to the point you are dendriting / damaging them severely. remember these are poly's not phosphates, that shit will take them out with just a few times and god only knows how many times it's been stressed already IF there are balance issues.
If you want to try to fix it, try to leave it run overnight again, otherwise, the only way to really see what is going on is to check the voltage on each bank in the overall pack. All it takes is one to get a little bit out and each subsequent charge pushes it worse and worse, and the ones around take a hit the other direction, until you are the point where you are having safety shutdowns if you have a decent BMS or severely lost range of travel.
Aaron