Here's an idea -- try and get your mileage re-deposited by CO. Claim that you got an EUA within the 24 hour period and that since they neglected to clear your upgrade in advance, and you got the notification that your upgrade waitlist expired, that you assumed your upgrade would be taken care of as part of the free unlimited upgrades that CO offers. I'm wondering whether they'll be able to tell what "really" happened from the PNR.

And by the way, how many total upgrades did there end up being on the flight? You made it sound like F availability kept dwindling with the 3 same people on the standby list, but it wasn't clear to me whether names started showing up on the cleared list (implying upgrades for those who hadn't checked in yet and thus weren't on the standby list) or not (implying last-minute F sales or flight changes, which wouldn't necessarily surprise me on this route). I think F buy-ups show as upgrades, no?