Depending on the setup in Item Maintenance, you can either explode the kit item to backflush the components, or not explode it and remove a pre-assembled kit from stock. I think you have a few options:
1. Have two items on the invoice: The original finished goods item created in BOM production entry, and the kit item that has negative components (the items being removed from the original production) and the replacement components.
2. You could ""reverse"" production entry, by using the BOM disassembly. Then re-produce the new item with the ""lower cost options"".
3. Configure the bill with the main components and using options. During sales order entry, the options can be selected so the product is customized.
If the process allows it, option 3 would require the least amount of work and subject to the least risk of error.