I've got the two options to pay back the full amount of the deposit and process it from your bank account, @karin8.
If you use an external platform to process payments in QuickBooks Online (QBO), you'll have to create a credit note. Then, enter a cheque to refund the deposit and record its payment. I'll guide you how.
To create a credit note:
The screenshot below shows you the steps.
To enter a cheque to refund the deposit:
View the screenshot below to guide you through the steps.
Once done, you'll have to record the payment by going to Receive Payment from the + New menu. Then, select the client's name. Hit the checkboxes for the credit note and invoice in the Outstanding Transactions section. After that, click Save and Close. See the screenshot below for your visual reference.
If you use QuickBooks Payments, you'll have to create a credit note by performing the first batch of steps above. Second, refund your client's credit card. Third, apply the credit note to the outstanding invoice. For detailed instructions, see the QuickBooks Payments users section through this article: How To Refund A Deposit And Close An Invoice.
Besides, I recommend going to the All Sales page from the Sales menu. It helps you view all the transactions of your client. From there, you can also edit, copy, send, void, or delete them. For more details, visit this article: View Sales Transactions.
I'm here to lend you a helping hand if you need anything else. Enjoy the rest of your day, @karin8.