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Hi Jwhits,
Thanks for posting in the Community! If a refund is not recorded yet on the duplicate payment made to the supplier, you can follow these steps.
After that, make a bank deposit to enter the supplier refund.
Once you create a bill payment, you'll be able to apply the deposit you've created.
For more detailed information, you can check on this article: Handle supplier credits and refunds in QuickBooks Online.
Feel free to drop a comment below if you need further assistance. Have a great day!