Yep, this happened to me, too, yesterday. I'm flying AUS-EWR-YYZ in H this coming Monday, both segments on 735s. I got the EUA e-mail yesterday at 120 hours before the AUS-EWR flight, letting me know that I got upgraded on the AUS-EWR segment. The e-mail showed all the proper segments of the reservation.

Then, a few hours later, I got an EUA e-mail about 120 hours before the EWR-YYZ flight, figuring I must have been upgraded there, too. That e-mail, though, showed only my original AUS-EWR EUA, and the EWR-YYZ segment entirely gone. I called co.com support, and they said the reservation is still there, although I wasn't actually upgraded from EWR-YYZ.

Weird....