I just had to do this in QuickBooks Online and figured it out. It used to be very, very easy to do in QB Desktop but it's not so obvious anymore and it had the pros stumped. It took me some searching and troubleshooting but I finally got it. Once you get to the create a check step (step #2) you can print the check out physically. Make sure the Customer info is up to date with how you want their name printed on the check. Note that if you already have a Credit in the Customer Account do not make another Credit Memo. Don't forget step 3 or it won't clear out the credit on the back end. 

Refund a deposit in QuickBooks Online

Not processed with QuickBooks Payments

To refund a deposit in QuickBooks Online, create a credit memo, create a check to refund the deposit, and then record the payment.

Step 1: Create a credit memo

1. Select + New.
2. Select Credit Memo.
3. Select the name of the Customer on your invoice.
4. Enter the total of the invoice, including the deposit, in the Amount field.
5. Select Save.

Step 2: Create a check to refund the deposit

1. Select + New.
2. Select Check.
3. Select the customer in the Payee field.
4. Under Category details, in Category dropdown, select Accounts Receivable.
5. Enter the amount of the deposit received in the Amount field.
6. Select Save and close.

Step 3: Record a payment

1. Select + New.
2. Select Receive Payment.
3. Select the name of the Customer on your invoice.
4. Make sure that the total credits equal the credit memo and invoice listed under Outstanding Transactions.
5. Select the checkboxes for the credit memo and invoice in the Outstanding Transactions section.
6. Select Save and close.