Doing the Credit Memo was the mistake; if, you already have negative AR from the double-payment, you just made another Negative AR using the CM. Delete it.
This is not correct: "and looks like I should do a credit for over payment instead a credit memo"
When you first got paid, you would have used Receive Payment and it was too much money = leaves negative AR. Or, you processed it anyway as Transfer fee, so yes, that is what you put on the CM, and you never had Negative AR all this time.
It's one condition or the other.
The name at total = 0 never shows on the AR reporting unless you forgot to Make the one from the other = they need to be linked. With the CM, there is an icon at the top to Refund; that Links them.
Or, you simply use the Transfer fee on the check to refund, and never needed all of this to run through AR at all.
To take ZERO names off of the AR Aging Summary, double-click their 0; here are the Unlinked transactions. Example:
You have an earlier payment and a later invoice, so now you open that original payment to Apply it to the new invoice, and their name disappears from the AR Aging Summary.
In your case, you use Receive Payment, leave the amount as $0 and apply the Available Credit to the refund check, which is a row like an invoice, because you listed AR on it.
Try not to do too many steps for any one thing.
