I do not have access to record a check bounce.  What other way can I tell the system a payment bounced?

Scenario: A customer sent a check we never received. They reissued the check.  Both checks then came in the same week.  We deposited both checks, but of course the stopped payment check bounced.  The good check is applied against the Invoice.  The bad check is listing as overpayment. What is the best way to clear the available overpayment.