I don't know if my situation is similar to all of yours. I booked a all UA metal ticket on co.com LAX-PVG, NRT-SEA-LAX. Then a few weeks later I noticed a schedule change on SEA-LAX leg. I talked to a CO agent to move that leg to an earlier flight, and after she made the change, she told me that she just noted something was wrong with my ticket and I would not be able to check in for my LAX-PVG flight.

I was on hold for about 10 minutes and she came back told me the problem was solved. There was a minor schedule change (1 minute) on the LAX-PVG flight, and that had somehow flagged the ticket as ineligible to check in either at the counter or online. Glad that I called.

So if a ticket is issued by CO, even a minor schedule change would make it out of sync?

I guess I'm right in the middle of a similar situation for the flights tomorrow.

Flying A-B-C-B-A on the same day, A-B and B-A segments on CO metal, B-C-B on UA with longer layover at C. I could check in only for the first two segments at T-24. I thought that C-B-A was considered as the return, but still can't check in for C-B-A even though T-24 for C-B has passed. co.com says I'm already checked in, showing only A-B-C. .bomb says to check-in through CO.

Come to think about it, I inquired about the upgrade on B-C segment because upgrade status still showed "pending" after T-100. The agent confirmed my upgrade not only on B-C but also on C-B although it was still a few hours before T-100 for that segment. I did notice later the itinerary page saying that the ticket must be reissued because of a change, and called CO to get reissued.