Deposit that doesn't match due to "non" refund

@PasadenaChamber 

"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.     

I followed steps 1 & 2, but for 3 I get a message that says the customer's "payment doesn't have an open invoice to go with it" so I have nothing to tie the payment to. It says if I want to record the payment without an invoice to "create a sales receipt". 

Also, this is not actually a deposit. It is a debit to my bank because the other funds received are less than the amount that was refunded, but I have to account for the payments and the refund in the same transaction.

@PasadenaChamber 

"I followed steps 1 & 2, but for 3 I get a message that says the customer's "payment doesn't have an open invoice to go with it" so I have nothing to tie the payment to."

If you're getting that message, then A/R must not be assigned to the check or the customers are not the same on the deposit and check.  When you go to Receive payment, it should look like this:

"Also, this is not actually a deposit. It is a debit to my bank because the other funds received are less than the amount that was refunded, but I have to account for the payments and the refund in the same transaction."

The other transactions creating the bank withdrawal for the day need to be entered too.  If you're not entering all the transactions for the day, then I guess I'm confused as to why this duplicate payment received and refund transactions are being discussed.  If you just want to create a withdrawal that matches the bank feed for the day, write a Check or use an Expense transaction for the amount of the withdrawal, assign the appropriate account to it, and match that to the bank feed.   

All of the transactions that make up the bank debit transaction have been entered. The "expense" portion I have entered as a refund and as a credit memo to see if one of them would show up as a match option on the list and neither do, and I do not know how to enter these transactions to get them to show to match. Additionally, the invoice payments that are part of this bank debit transaction are all entered, but because they are income/payments, they do not show up on the list of transactions available to match because QBO only pulls expenses for a debit.

My CPA has been working on this for a couple of weeks and their conclusion is that it will take several journal entries to get everything to match and then to remove all of the entered transactions that cannot be matched because QBO does not pull them up during the matching process.

This is an unusual situation since we use a 3rd party software for A/R and have to manually enter the invoices and payments into QBO since the CRM doesn't properly integrate with QB.

Thanks for trying to help!