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The unapplied ACH payment, which is normally shown as a deposit in the customer's profile, is already saved as a credit/overpayment. It debits the bank account and credits the A/R by default.
I recommend sending a statement to your customer, showing their balance including the unapplied deposit because we can't just simply convert that deposit into a credit memo. It would require moving the deposit amount from A/R (deposit) to a clearing account, then back to A/R (as credit memo), which is not normally done in QBO.
Create a statement:
Alternatively, you can create a temporary credit memo and send it to your customer. Then, save a PDF copy of it, attach the copy to the deposit (ACH payment), and delete it afterward.
Let us know if you have other questions in mind.