Every effort should be made to make Player B whole by reestablishing his chip stack to the amount that it was at the break, less any blinds the he would have paid while absent. Hopefully, Player A's correct stack has chips sufficient to correct the damage made to Player B's stack. If all of Player A's chips are needed to make Player B whole then Player A is out of the tournament.
Obviously, this is a serious matter. I doubt that it would have been done on purpose but I would most likely penalize Player A if he was still in the tournament so that it doesn't happen again.