Supplier took overpayment

A Supplier was overpaid on our credit card (supplier took too much), I processed the payment at the amount they took via pay bills, which left an overpayment on the system.  The supplier refunded the overcharge.  I have entered a credit card charge (credit/refund), but there is now the full initial payment showing as a credit on the supplier's account, as well as the credit card refund.  If I go into pay bills and set the credit it then makes the supplier's account show as being in credit for the original amount (as if the original bill has not been paid).  I cant get it to balance and dont know what to do!

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