It sounds like you’re trying to figure out a way to allocate costs to output for leftover stock that has already been shipped and invoiced. While it may not be possible to replicate the exact functionality built by the previous partner, there may be some workarounds you can explore.
One idea is to use the Item Charge Assignment feature to allocate costs to the output of finished production orders. This would involve creating a new item charge code specifically for the leftover stock and assigning it to the output items on the production orders. The consumption of the leftover stock would be treated as a write-off of inventory, but the cost could be allocated to the output items and flushed through similar to item charges.
Another option would be to create a custom journal that would allow you to manually adjust the costs associated with the finished production orders. This would require some development work to create the custom journal and integrate it with the production order process, but it could be a viable solution if done correctly.
Ultimately, the best solution may depend on the specific needs and requirements of your customer, as well as the limitations of their current NAV2013 system. It may be worth consulting with a NAV/BC developer or consultant to explore different options and determine the best course of action.