I agree with HeathrowGuy -- if the check-in system says your reservation is "out of sync", it's a good idea to call the reservation agent to get things resolved.

A case in point is my experience with an out of sync reservation last weekend. The last UA flight of the day out of ROA was canceled, and when I called UA reservations for rebooking I was transferred over to US flight out the next morning. When I got home, I went online to check in for my new flight and got that message.

Fortunately I called, as apparently UA made mistakes in reticketing my reservation with US. In part, UA's reservation system showed me properly rerouted ROA-PHL-LAX, but the ticket record in US's system show me routed ROA-PHL-SFO ... not where I wanted to go. After 30 minutes on the phone, first with US and then with UA (since it was UA's problem), they said it was being fixed and I could check in the next morning. Alas, it was not to be, as my reservation was still out of sync at 6am. It took another 45 minutes on the phone to finally get it resolved, with most of the time on hold with UA -- I think that was mostly them trying to coerce US inventory control to free up a space for me on the flight I was supposed to be on.

The lesson is that I'm glad I called to get the problem resolved when I first saw it at OLCI. If I had arrived at the airport the next morning expecting to be able to check in there, there likely would not have been time before my flight for ticketing to fix my problem. Also, there would have been less chance of them being able to find space for me on my proper flights when it was that much closer to the departure time.

[BTW, after all this, I still never made it to LAX that day. Even though I was booked on the 11:15a ROA-PHL flight, both that flight and the next one were so delayed by maintenance problems -- each over five hours -- that I couldn't make the last PHL-LAX flight so I then had to overnight in PHL.]