I had once a horrible experience on a Barranquilla-Panama-AMS flight. I upgraded with miles for the PTY-AMS leg on KL. They made the stupid error to remove the whole flight and only reinstall my PTY-AMS leg in business. I somehow could check in electronically from Baranquilla-Panama (executed by Copa) but then was refused boarding (with 35 min to go) at the airport since they said that leg was deleted in their systems. Frantic mailing, facebooking and calling just saved the issue before doors closing........I got a few 1000 miles as compensation for my horror experience after I complained. If you have proof (screenshots, emails) your rebooking was sound, I simply would contact customer service. If your rebooking was eligible and sound according to the information you had, you should not be in the situation you found yourself in.