Check was unused by vendor but all invoices paid

SOLVED

I recently took three checks to our local tax office to get registration on vehicles (five vehicles on each check).  I got the registration costs from the tax office website.  However, I was told that I had overpaid by over $500 dollars.  Instead of giving three refunds (one for each check I had taken them), they used the two largest checks to cover everything and handed me back the third check that they did not use.  How do I handle this on the books?  All 15 invoices were paid, but not necessarily using the check that I had cut for them.  And if I void the unused check, now I've got five invoices that will show unpaid.  Any help will be very much appreciated!!