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Banking
"The second invoice, payment and refund, I have not entered, because QBO would then invoice as unpaid and outstanding. If you enter a credit memo, same thing."
If I'm following your process correctly, try this:
1) Enter a deposit assigned to customer's A/R for the duplicate invoice payment received.
2) For the refund, use a check transaction (New > Check) and again assign it to the customer's A/R.
3) Tie the two transactions together by going to New > Receive payment and apply the check to the deposit.
You should now have the deposit and refund to match to the bank feed.