Hi MarkIf the transaction has been entered as a Cash Receipt and you didn't ran the "Paid transaction removal" routine, you can just void the transaction by going into Sales >> Transactions >> Posted Transactions. That will result as a negative cheque amount in the deposits for the checkbook. Just redo the cash receipt transaction with the correct customer, go do the deposit with those two cheques (deposit at zero) just make sure to select that deposit in the next bank reconciliation and you will have fixed the problem without affecting your bank reconciliation.
If the transaction has been entered has Bank transaction see Brett Albrecht answer
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