I have this occur all the time. A customer will take a discount or decide they were not paying for an item on an invoice after it has already been paid. Go back to the first payment. Receive entire amount but only apply the amount paid less the subsequent discount. You do this by typing in the amount in the right hand column of the invoice list. This will leave an open credit. Receive the 2nd payment and apply it to the 2nd invoice. This will leave the invoice partially paid. Click on the DISCOUNTS and CREDITS button at the top of the receive payment screen. Apply the open credit to the 2nd invoice.
I like to scan and attach copies of the check and voucher portion so if there is a question down the road, I have a visual reminder at my fingertips without having to search through paperwork.
