I issued a check to refund an overpayment (deposit) how do clear it?

Hello there, @SRay1.

The overpayment may haven't linked to the refund.

When you have issued a check, you can follow these steps to link it with the overpayment.

1. Go to the Customers menu and then select Receive Payments.
2. From the Received from the drop-down, select the Customer.
3. Then, select the Discounts and Credits icon.
4. In the Available Credits section, select the check you created and then Done.
5. You may see a prompt to Confirm transfer. If you do, select Yes. The amount will be applied automatically to the invoice.
6. Select Save & Close.

You can check this reference for the detailed steps: Give your customer a credit or refund in QuickBooks Desktop for Windows.

Ready to reconcile your account after dealing with the transactions? You can check this article for the workflow guide: Reconcile an account in QuickBooks Desktop.

Feel free to place a comment if you have other concerns with recording transactions in QuickBooks. I'm always here to help. Have a great day!

This worked perfectly. Thank you so much for your awesome help!! :)

So glad this solution worked for you, @SRay1.

Please don't hesitate to reach out with any other questions you may have. 

Have a fantastic weekend!