How to add non-stock lines for a future shipment

With the current supply chain issues we frequently have to split our orders, which works great for stock items, but we also have to split the freight and activation charges, which is done by adding an additional line in the order. The orders management team wants to add the freight for the 2nd shipment at the time that they release from backorder the portion that is to ship now. If they do this the freight or activation charges for the 2nd shipment get pushed through to invoicing based on the Order Activity rules. How can we stop the