Hello. I have the same problem with refunds that are mixed in with the payment batches from our point of sale - The way I work around to balance to zero is by:

1)create a credit memo for the product or service you are refunding ( this will put the customer balance to a negative)

2) when creating a deposit by matching the payments of the customers, after you have found all the payments from the customers for that deposit, you will have a difference in the amount of the refund (or refunds combined) you can resolve the difference at the bottom of the page by creating expense(s) to the customer(s) through accounts receivable for the amount of the refund(tax-out of scope). *now your customer balance will still be off

3) RECEIVE PAYMENT FOR THAT CUSTOMER - this will match the expense (for a/r) and the credit memo(for product return) and the amount of the payment with be $0 - at the end your customers balance will be back to zero.

It is a pain to do (I agree) but I have not been able to find a faster solution myself. If only refund receipts showed up in the transaction matching of the bank deposit

Greg