There are programs who will check to see if your scores are out before they rank you. And if you fail, they will not put you on their rank list. I would check with each program. If they asked about level 2 at your interview, I would worry. If you really don't want to mess up your rank list, then contact them after rank lists are due. I do know that during my third year, the PD was checking in the days before rank lists were due and darn near their exact words were "well, now that failing step 2 scores are coming in, our rank list is changing because we don't rank anyone who fails step 2 this close to match." And not a competitive residency either.
I would contact your Dean's office regarding the ramifications. They will likely be able to help you more than we can as they have specifics regarding your match list. They may have run into this situation before (in fact, likely) and may know answers to your questions regarding the specific programs on your list. You may be fine. You may have problems. This will likely be very program specific.