Here's the setup: You have a space station orbiting Earth. On this space station is an anti-gravity device powerful enough to lift a small ship on Earth up through the atmosphere and into the space station (or next to it, anyway). Disregard for the moment how such a device works or came to be.
The problem with this highly convenient technology is that it essentially creates a column of reverse gravity (gravity going against Earth's natural gravity - that is, up) from itself to the surface of the Earth, wherever it happens to be pointing. This means that anything in that column of reverse gravity is going to be sucked off of Earth and into the space station, including the ship it's targeting, any unfortunate individuals out for a scenic flight, and all the intervening air.
It's the air I'm concerned with. What would happen if a column of air was abruptly sucked into outer space? Since the space station is close enough to be orbiting Earth, I would assume the gases making up the air would eventually return to the atmosphere, but what would the effects be in the meantime?