PwC:

I have a client with the same issue.

One thing that has helped is to check the boxes in the company profile to allow "Credits on Invoices" and "Edit Invoiced Orders."

The cannot edit any of the order lines that have been invoiced, but they can return/credit them by entering the same SKU with a negative quantity shipped. They they enter the corrected item/price/misc charge etc. and a new invoice is created for which they can enter appropriate payment information.