Most international flight don't allow online check in for precisely this reason, everyone has to get their passport verified. Good luck with the I'm picking it up mid trip argument!
Most international flights? That is some strong language, I haven't checked in at a counter in a very long time, although I have been asked once at security (I only give my ID usually in the states, and OP doesn't have to show the second ticket to the agent), and I have only been checked right before boarding the international flight. I have over 100 boarding passes on my phone.
OP, will they let you check in online?