Yes. The court can't kick out suits where the defendant doesn't show up, unless the suit has no basis in law. In this case the suit might have a basis if the payment was recent enough, so it requires the defendant to stand up and say "No, the payment was made on this date and that's outside the limit.". As soon as the defendant says that the judge can dismiss the suit, but before that he's got no evidence to support dismissal.
And no, there's no penalty for filing. There is, however, a penalty for failing. If the bankruptcy trustee does this several times, the judge can penalize him in any number of ways. The nicest is to require the trustee to present all the facts about every payment he wants to recall and get the judge's approval to go forward with it. The nastiest is for the judge to invite the defendants to file for costs and fees (he usually can't award them unless the defendant asks, but when the judge invites you to ask for them it's a sign he wants to award them), and since this all happens after the bankruptcy was filed the judgement would go ahead of creditors.