Before you consider recrediting your customer's (the drawer's) account for the amount of the mistakenly paid check, keep in mind that under Section 4-403(c) of the UCC:
"The burden of establishing the fact and amount of loss resulting from the payment of an item contrary to a stop-payment order or order to close an account is on the customer. The loss from payment of an item contrary to a stop-payment order may include damages for dishonor of subsequent items under Section 4-402."
What was the check for? Was your customer obligated to pay the payee? Was there really a loss to your customer? If so, you will probably be liable for the extent of the loss caused by your payment over the stop payment order, but you will then legally stand in the shoes of your customer to proceed against the payee. So, if the payee was accidentally paid twice, for example, you can proceed against him to get back the overpayment.