How to unlink a bill payment from a cleared check

Hi,

We had a vendor issue a bill (For the sake of this example let's say the bill was $100) to us for a replacement item that would later be offset with a credit (For the sake of this example let's say the credit was $100). When the vendor issued the bill they included a quickpay discount. We paid the bill before having received the offsetting credit, using a check, taking the quickpay discount ($98 payment with a $2 discount applied).

The vendor deposited the check upon receipt, but decided that the quickpay discount was an error. So to correct this on the vendor's side, they've offset the bill with the matching credit, and left the check we sent them as an over payment (credit) in their system. 

I now need to modify things on our end to match, the easiest way I can think to do that would be to change the check so instead of it showing as paying the original bill, it shows as a credit on file - But I can't seem to figure out a way to do that.

If anyone knows of a way to accomplish this, any advice would be greatly appreciated.

Thanks,