It appears ShipStation, as validated by tech support, does NOT allow users to edit the order items whatsoever when imported from a sales channel. I think this is nuts. The "Apply changes to open orders" does not even give us that magic override - it does nothing.
This is crazy, as the owner or operator I know what is best for my customers - not ShipStation. If a product needs substituted, let me. If you're out of stock, and there's another idential SKU (or two SKU's) or a Bundle you want to send them instead, let us make that change on the fly.
The only workaround we could figure is to deactive an out of stock SKU, then manually add bundle items, for every single order. Instead, if the system had let me update the existing out of stock SKU to a bundle, and then populated the bundle items to each order as implied by the "apply changes to open orders" selection, I would have been making customers happy instead of troubleshooting for hours.