So, to wrap up the story, after two calls to AC and six to Avianca I got nowhere. I had to go to the airport without my check-in done. At the Avianca check-in counters they were only able to give me the boarding pass to BOG, but not the following flights with AC. Which made me lose on an upgrade (as they didn't even check me in), and also forced me to go through immigration at BOG, go to a check-in machine, get my boarding passes, and go back through immigration and security.

Clearly the AC/Avianca IT relation has some significant kinks to iron out yet.