I have had several bookings that were latitude cash with confirmed eUpgrades from non R stock cancelled because of AC schedule changes. When I call in to discuss rebooking options, I have been told that the agents can't see the availability (or incorrectly claim there is no availability because there is no R space). The problem is that every agent (except one SE agent one time) tells me that I only get one complimentary change without fare adjustment and if the eUpgrade on the new booking doesn't get immediately confirmed I'm out of luck and must stay waitlisted or pay to try a different flight.
In these scenarios, the online rebooking tool, and also agents I might have interacted with have normally protected the upgrade (with agents I would make sure that was indeed the case and they would confirm - note that I have access to the SE priority phone also). This regardless of upgrade inventory availability.