I am confused as to what kind of upgrade you used. Was it a Confirmed Regional Upgrade (CR-1, electronic), or was it something else?

The only time I have had a confirmed upgrade become unconfirmed was when I was not eligible for an upgrade (1700 mile flight, 1000 mile upgrade) and once on a eqiup swap.

If this was a three class plane as you say, the smallest it could be is a 757, which is the normal a/c. So any equip swap would be in your favor...