This has actually happened me several times -- that's why I view My Intineraries daily. I even managed to catch a seat change on my OXR-LAX-ORD-FRA-FCO flight in Jan, just ten minutes after it happened. I dutifully called CS and was told that my upgraded seat in C could not be changed . . . until I nicely suggested that we talk to someone who can make this happen. She contacted a supervisor and the problem was fixed.
I have had simply horrific problems with an itinerary I made through Amenity. The changes made to the itinerary and to the upgrades by UA has been both infuriating and frustrating -- as well as costly -- because you must go through Amenity and not through UA... It was on an upgraded C 2-for-1 ticket to FCO (same ITN as above, different dates) and the planes, flights and seats have been changed no less than four times. It has been a battle just trying to maintain the upgrades, when changes are made.
I remain ever attentive to My Itineraries....