Real Negative Receipts

We have customers that accept credit card payments from their customers.

We process our customers bank statement through our lockbox, and apply their customers credit card payments to our customers invoices.

Clear so far?

Once in awhile, we will receive a negative credit card payment from the bank statement, because one of their customers returned a big item, and the total for credit card purchases for the day were negative for our customer.

Lockbox does not accept negative amounts.

What is the best practice, manual or otherwise, to reconcile these types of transactions?

Do we issue a negative miscellaneous receipt against something? and then issue a debit memo (or invoice) to our customer?