I am not sure which program you are applying to or what the correct course of action should be in your situation. However, if it helps any, I do know that they can refund application fees paid by applicants if the department head requests it (at least in regards to apps submitted through the Vanderbilt Graduate School Application). It can take a while though to get the refund back.
If you need the money soon, it might be better to just wait it out but if you're worried about the deadline and don't have financial concerns, might be better to go ahead and get peace of mind by having all the boxes checked by the deadline.