I had been in this sitaution once and it did not work that well for me. Normally EUA happens before you do your nwa.com check-in. But for a recent trip, at the time I checked in online 23 hrs before the trip, I got the upgrade for the first segment. For some reason, the EUA for the second segment happened after I checked-in and I was actually up-graded, (which I didn't know, until after the trip, and i checked my email). Upon enquiring at the gate for an upgrade, I was told by the gate agent that the FC is full. And when I was boarding for my previously selected exit-row seat, I was told I am not assigned to that seat, and that seat was also gone for someone else. They managed to find one seat for me on that fully booked flight, and I think they alloted my upgraded seat to someone else or a crew member. So, checking in too early could be a draw back in rare occasions like this. I cannot generalise this, as I also beleive it had something to do with the 'not-so-friendly and unco-operative' gate agents at Memphis for that particular flight. Otherwise they could have found this out, when I enquired about the upgrade at the gate.