I went through something like this in BOS on Thursday. My flight got delayed 30 minutes, but appeared to be headed for a delay much longer than that (wound up being four hours, good guess on my part), so I called the medallion desk and asked for a rebook. They rebooked me and everything looked swell on the Delta app, until I looked at the upgrade list. I wasn't there. Trouble. Tweeted, discovered I wasn't checked in, tried to check in, couldn't check in, went to the airport early.

At the airport, the agent told me the phone agent issued a new ticket, on the same old PNR, but only put one of the two segments I needed on the new ticket. It took a phone call and a good 25 minutes for it to be worked out.

All of this is to say, beware what the phone agents do. The agent at BOS said she had no idea how an agent could screw up a ticket so badly.