My client paid me by check, but when I went to write off her invoice, I said it was a check, but she was charged as an ACH, meaning there was duplication.

Processing ACH refunds depends on whether the payment includes a convenience fee, Igor.

ACH refunds aren’t available for payments without a convenience fee. Refunds must be issued using alternative methods such as cash or check.

For payments with a convenience fee, ACH refunds can be processed through the Merchant Service Center after 5 business days. Refunds processed on the same day will void the payment. Follow these steps:

1. In the Merchant Center, go to Processing Tools.
2. Select Refund an eCheck.
3. Set the date range for the payment, then click Search.
4. Find the transaction to refund or void, then hit Submit.

Afterward, you'll have to update your QuickBooks records manually, as refunds from the Merchant Service Center don’t sync automatically. Refer to the Refund a customer's ACH payment section in the article Void or refund customer payments for the detailed steps.

Also, you can configure customer payment method preferences to prevent duplicate payments in the future. You can do this by navigating to the customer's profile and clicking on the Edit button. From the Payments section, choose the Primary payment method. Check out the image below for visual reference. 

If you have any questions or concerns, feel free to comment below.