Parent & Sub Customer Paid; How to Refund Sub-Customer?

To fix this:

- Edit the first payment you received for the Job (sub-customer) and de-select the invoice it pays and save it.

- Edit the second payment from the Customer and apply it to the now-available invoice for the Job.

- Create a refund check by writing a check to the Job and using the AR account as the "expense" account. This will create what looks like an invoice in the AR account, increasing the account balance for the customer up to 0.00 (assuming no other unpaid invoices on account.)

- Edit the first payment again and apply it to the refund check, which will appear as in invoice to pay in the table of things to pay.

My co-worker, who typically handles receiving payments and does our monthly bank reconciliation, thinks that changing the original payment will mess up our books because the check has already been deposited and reconciled with the bank. So she opted to:  set the sub-customer up with a vendor account, create a "bill" from the vendor account, and write a check to pay the bill, and charged our "Sales" income account for the payment. This seems okay, except that now we still have an "unapplied ar payment" sitting on the Parent customer's account in our books. What do I do now???

Undo what your co-worker did and do what I recommended.