This deflate gate issue is probably a big factor for loosing an upgrade. I suspect it happened to me on a CDG-YYZ awhile back. I was confirmed up until a few hours before departure. I was told the seat I was assigned was written up as unserviceable. The flight was full so I was punted to the back. Something to keep in mind when thinking your "good to go" with your upgrade!
I even told the concierge I would take the seat even if it was the deflate issue, but she said it was already written up so it couldn't be used...arrrggg!