Amount due on invoice payment slip not reflecting credit notes applied

Hi - I have a customer who double paid an invoice. I issued a credit note and applied that to their next invoice. However when they were sent the invoice although the email shows the outstanding amount the full amount shows on the invoice and doesn't show that there was a credit against it and only a small balance. Consequently they have paid us the full amount again. I did draw it to their attention in the covering email but they have obviously gone on what's showing on the invoice. How can the outstanding amount be shown on the invoice. It doesn't make sense that the payment slip is showing the original invoice amount and not the amount actually due.