Thanks for reaching out to the Community, Majestic Pools. I appreciate the screenshot, that helps me to see what's going on.
When you refunded one of the duplicate payments to your customer, a record was automatically applied to the invoice. Additionally, both of their transactions will be displayed on the one they paid. So that part should already be looking accurate. In regard to the other customer's transaction, there shouldn't be a problem with your records. They paid what was owed, and there was no overpayments/refunds, etc.
Ultimately, the two original payments were deposited, as was your additional one, minus the credit taken from it. What you'll want to do is leave everything as it is. The refund is already applied to the proper invoice/customer. You wouldn't want to apply it to a client who didn't actually receive one. Everything works out with your amounts, because you still received the same amount of money that was processed.
What you can do, if you'd like, is add a notation to the customer's invoice (the one that was offset from, or both of them) pointing out what's taken place.
Here's how:
1. Open the customer's profile, then their invoice.
2. In the Notes section, click the Pencil (✎) icon to add notations.
3. Enter the details you'd like attached with your record.
4. Select Save & Close.
Now you'll have a relevant entry in your books showing what took place.
Here's our resource archives for QBDT, this may come in handy moving forward: Help Articles
If there's any other questions, I'll be here to help. Have a wonderful day!