This is definitely an accounting question, not a systems issue.
We have had several clients in the business of buying bulk lots of inventory, breaking down the surplus purchased and then preparing some for resell and others for disposal or storage. We had one client on MAS 90 who had been a family owned business for years and played fast and loose with inventory valuation for items purchased in bulk lots. They would adjust the value of the item sold at the time of sale to minimize taxes. We always told them that this was not in compliance with GAAP and that they were opening themselves to possible problems with the IRS and lenders. However, they were small and ran the way they wanted. Since we weren't their CPA's, they nodded nicely and did what they wanted.
Then one day, they went public and sold stock in their company over the counter. When asked how to better automate inventory valuation adjustments at the time of sale as their business volume had grown significantly, we had the discussion of proper valuation methods and allocating valuation of items at the time of purchase. Once again we were dismissed out of hand but this time they changed VAR's to someone who was not a CPA.
Our vindication came several years later when we read in the paper that the company was under investigation by the SEC for fraudulent accounting practices relating to inventory valuation.
The moral of the story is that the items should be valued at the time of purchase at the lower of cost or market. If the purchaser buys a lot of 1,000 items and believes that only 100 have a commercial value, then set up inventory that way. They would set up 100 times or 1 item with a quantity of 100 with the cost of the lot allocated across the items. The remaining times can be stored in the warehouse / yard and not put in to inventory. When sold, run them through as a miscellaneous item without a cost. The proceeds are pure profit as you essentially sold scrap material. If you really want to track the non-valued purchased items, set them up as items without a cost.
Good luck.