Retail B2B Customers taking invoice deductions

I have a customer in the retail apparel industry selling to big box and high end sporting goods stores.  As a rule, their customers deduct charges off the invoice (saying things like product was damaged, shorted, etc).  We would like to be able to clear the invoice (instead of leaving the amount open) but be able to track the deductions so that they may be able to collect some or all of the deduction if possible.

Only way I can think of is to do a credit memo with some sort of a custom field to show it was a customer deduction and somehow report some sort of an aging report.  I know this was a huge issue with dealing with grocery chains but was surprised it was prevalent in other B2B industries as well.