Chanding a Work Order Part number assignment midstream in the routing steps

What would be the best approach to handle work orders that start off as Part X and half way thru the process we determing we really need part Y.  There are Approximately 100 components on the bom and we're using lot numbers, so reversing the steps, and material and reducing the wo qty is a complex process.    Currently the users are moving the qty to the scrapped column, completeing the order and creating a new work order using the partially completed parts.  This action is skewing our scrap and yield data that pulls from Type 5 hours.  Other times they