Before you can issue the refund you need to receive the money.

•  find the client and select "receive payment"
• Add the overpayment - don't match it to anything, don't create an extra invoice
• Save and close...you'll get a message "We'll save this payment as a credit to your customer since you didn't select an invoice." click "Save as credit"

Then follow the instructions from Intuit:

Note: If the customer has overpaid – you do not need the credit memo as you will already have an unapplied credit that acts as your credit memo.

1. Select + New and select Expense.
2. In the Payee field, select or enter the desired customer.
3. In the Payment account field, select the bank the money is being refunded from.
4. In the Category field, select the Debtors account (Accounts receivable).
5. In the Amount field, enter the amount of the refund.
6. In the Tax field, select the appropriate Tax (not inclusive/exclusive of tax).
7. Select Save.
8. Next, go to + New and select Receive payment.
9. Add the Customer and choose the Payment method and Deposit to.
10. Balance should be 0 as they will cancel each other out.
11. Select Save and close.
12. If you have Online Banking, go to Bookkeeping then Transactions then select Bank transactions (Take me there), or go to Banking (Take me there). Then match the record you found.