Hello there, @SaaSam.

Thank you for joining this thread. I can share some insights about refunding or deducting a deposit.

You can record them as a credit card memo, I'll show you how:

1. Click Customers.
2. Select Create Credit Memos/Refunds.
3. Select the customer name.
4. Enter the necessary information.
5. Click Save and close.
6. On the Available Credit window, choose one of the following:
   • Retain as an available credit 
   • Give a refund
   • Apply to an invoice 
7. Select OK.

To provide them the amount, you can either issue a refund through the Receive Payments or Write check window. For detailed instruction, please use this article as a reference: Record a credit memo or refund in QuickBooks Desktop.

I also recommend seeking an accountant for an expert's advice to ensure there will be no problem with the books in the future.

That's it. Let me know if there's anything else you need, SaaSam. Just add a comment or mention my name. Have a good one.