Your lipo puffed cause you overdischarged it, 4.04v is 2.02v/cell and cells should never go below 3v/cell or 6v for a 2S.
You can try charging it as NiMh, but I would use a lower rate like 0.2 - 0.3amp so there is as little chance as possible that charging could cause more swelling. If you see it swelling more while trying to get the voltage back up, stop charging immediately and remove the lipo to somewhere it can't hurt anything if it goes off.
The lower charging rate will make the voltage come up slower and more evenly, let it charge until its comfortable over 6v. I usually try for 6.1 or 6.2v before I stop and then finish charging it as a lipo using lipo balance charge mode. You might be best not charging it at a full 1C rate thios next time too and watch it carefully while charging as a lipo for more swelling.
If you do manage to save it, its prob been damaged by dropping to that low of a voltage, so don't be surprised it isn't as strong as the other. The big ques is why the lvc did not kick in and stop. You didn't see it slow down even a little? I can see mine slowing before the lvc hits and thats when I stop. I wouldn't run again until you know why the lvc didn't work.