The simplest method would be to issue a credit memo for that customer.

Depending on how the original invoice posted sales and sales tax payable (since you aren't using the QuickBooks defaulted platform), you would credit against . . .??

The dating issue comes into play here as well... were these invoices in a time period that you already paid/reported on?

I suggest that you ask your accountant for advise on this one.

Hope this helps