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Buy nowWe appreciate and value your feedback, @KSMiller.
As of now, manually editing the transactions is our only option to have a reliable record of the account's revenue.
While I understand the convenience of converting a declined sales receipt to an invoice, QuickBooks Online (QBO) is designed to record an invoice only as a pay-later transaction and a sales receipt as a pay-in-real-time entry.
I encourage submitting a formal feature request to our product engineers within your QBO account, especially about running reports for outstanding balances due for declined payments. This way, your suggestion will highlight where the software needs to improve.
For future reference, I'll add a guide here if there is a need for issuing a refund for a customer's overpayment or credit: Record a customer refund in QuickBooks Online.
You're always welcome to visit the Community again if you have any other questions. We'll do our best to help you.