Pleased to hear again from you, @Smak1.

Let me take this opportunity to furnish you with information on how you can issue a credit memo to your customer.

Here's how to create credit memo:

1. Click the Customers menu.
2. Choose Create Credit Memo.
3. Select the name of the Customer:Job.
4. Enter the credit memo details.
5. Click Save and Close.

There's no need for us to write a check to denote the refund amount since it's already recorded in your QuickBooks when you made a deposit as adviced by my colleague, @Alessandra_B.

Let's proceed to linking the credit memo to the unapplied refund check. Here's how:

1. Go to the Customer menu.
2. Choose Receive Payments.
3. From the Received from drop-down, select the Customer.
4. Go to Discounts And Credits.
5. In the Available Credits section, mark the check you created, then select Done.
6. Select Save & Close.  

That should do it! Don't hesitate to visit here in the Community if you have other questions about processing customer's refund. I'm always here to help.