Subcontractor for manufacturing operation that is also an intercompany supplier

We have an intercompany supplier that is used every day as a subcontractor for many, many various parts to process for an operation (to galvanize) which then become a different PN upon receipt. The incoming PN mix and qtys never equal the outgoing, so much of the recognition of inventory movement is done on the back end, with varying timeframes, etc., and causes chronic inventory inaccuracy.

Does anyone else have a similar scenario, and are there any lessons learned to share? Any setup considerations that affect success?