I am having an issue with an expense on my bank feed. Our A/R is run through our CRM, but all transactions are entered into QBO. The CRM is weird in that a customer may be billed twice for the same item and if both invoices are paid and a refund is issued for the "overpayment", you do not "write-off" or zero out the second invoice that was paid. (I don't understand, but that's a whole other issue). 

Anyway, a client was double billed and paid both invoices. I entered only the first invoice and payment, deposit (all funds received by CRM each day are direct deposit into our bank) matched, all good. 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. 

In this case, we were actually charged by the CRM because the refunded amount was greater than the payments received that day. I cannot figure out how to enter a transaction that will match to the bank transaction that does not mess up the accounting. Every way I have tried to enter it, there is nothing to match the bank transaction and I have an open invoice.