Can an A/P Credit on a Supplier be applied to a Customer's Penalty deduction in A/R?

We have a situation where a third party warehouse (Supplier) that ships our product to one of our Customers over-shipped the quantity and then the Customer deducts a penalty for the over-shipment. We want to credit what we owe the Supplier and apply against the deduction the Customer puts against their Invoice. I have read the A/R - A/P Netting and it appears to only work on for the same Customer/Supplier number.