the more likely reason you'd lose your upgraded seat is because of an equipment change, to Ted.
i had a 6-segment domestic itinerary in january, all upgraded Y -> F via CR1s, all upgrades confirmed more than a week before the flights.
for 2 planes (segments), there were last-minute equipment changes (to Ted, no F cabin, they told us as we were boarding) and i "lost" my upgrades (one was DEN/SFO, which is a route i don't even think Ted normally flies!).
as a "one-time-only show of their appreciation for my business," UA redeposited 1 CR1 into my account. that's all i got out of it.