This is a little tricky due to timing.  You could just enter the second invoice/payment the same as the first and then enter a 3rd invoice as a credit to reverse the duplicate payment.  then post a 4th positive invoice for the refund, down in the grid code it to the checking account so it acts like the deposit.  Then apply the credit to the refund as a manual check.

Or just post the second payment using the date of the payment, as an invoice and code it to the checking account, then pay it.  Leave it as a open on the bank rec, until they credit you next month.

Thank you for your help!