Originally Posted by FlyerBeek

Assuming it's a connection (and not stopover) in JFK, you should be fully entitled to use Flagship check-in. Whether your name will be on the list is a different question, but if you're stopped I would just politely remind the bouncer that you just arrived in Flagship/International F. Once you get to the actual check-in agent, you shouldn't encounter any resistance.

-FlyerBeek