A client had late deposits, blah, blah, blah. Anyway, the calculation could not be done in time so we filed Form 5558 to request an extension for the 5330 along with a check to cover the taxes that would be due. Now that we have finally finished the calcuation, there is an overpayment of taxes. How do you go about getting this back? The instructions to the form 5330 say to file an amended return. Well how do you file an amended return when you haven't even filed the original?

This happened to me a couple years ago. I wrote a letter to the IRS explaining the overpayment, and a "refund" check arrived a couple months later.