Hi NS-01
If you already have invoices owing to the Supplier, then you can go to the Purchases Register and then click on the Returns & Debits tab and apply the credit note to one of these. Otherwise, you can do this after you process the next invoice or apply the credit note when you go to make payment. The end result will be the 2 invoices that were paid, less the credit note for 1 invoice that shouldn't have been paid, meaning the account will come back into line. The bank reconciliation will reflect what has actually happened, including the incorrect double up and the credit note that is applied to payments to correct this.
If you are able to make a test desktop file COPY to temporarily test this (delete it afterwards), you will be able to see what happens and then you can process it in the live file.
Cheers
Liz