Customer Material Payments

How do others handle payments for materials that you have bought that you are building into their product and the excess material effectively becomes customer managed (Owned) inventory?
If the material is in stock we just ship that material to the customer, invoice and then bring back in using the EPICOR CMI process of PO and receipt into Customer Managed Bin. However if all the material is already in a job, that is when we hit an issue currently!