I think in this case the "check-in" button is mapped into the "eject" button and you will be out the window.

Seriously, I would check in. Far more likely to fix an issue that break anything. Sounds like they just re-booked you as if you had a stopover and really are not checked in for that flight.

If you do not elect to check in, go to the gate when you land and checkin, or prepare to lose the flight.