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Hello @pd2020,
Ideally, the system is unable to refund the actual money back into your customer's credit card account. If you wish to do so, I'd recommend contacting your payment service provider so a specialist can help you process the refund.
For now, we can consider recording the invoice payment and create a refund receipt inside the system so you can keep up with your records. To start with, let's open the invoice and click on the Receive Payment button to close it.
Once done, here's how you can create a refund receipt:
In addition, here's an article you can read to learn more about how you can manually create a refund: Record a customer refund in QuickBooks Online.
Lastly, I've got you this helpful article for ideas about how you can manage all your sales transaction: Invoice Tracker.
If there's anything else that I can help you with, let me know in the comments. I'll be here to lend a hand.