Turns out the flight was overbooked, offered $1600 to fly the next day, which we painfully had to turn down because of firm plans. Seats got screwed up but I guess they blocked some of the bulkheads for the airport so we ended up with decent seats on the longhaul which is all that really mattered.

Still not sure why I would be able to continue online check in online but my companion could not. Not impressive IT.