If I'm swimming in the 890 Jump swimming pool and the gravity generator gets destroyed, what happens to me and the water in the pool? And will we see a difference between space and atmosphere?

That is a very difficult question. I would suggest that the water will probably be sucked out of the pool very quickly to avoid a Passengers-style drama happening. As cool as that might be, that terrifies me as a non-programmer. That's really hard. Obviously, if the ship's in gravity, and it's less about space and atmosphere, I assume, where this question is going: gravity in a planet and the gravity drive on your ship goes off.

Does the water stay?

The water stays there. That's in the planet gravity.

How about if you're flying upside down?

If you're flying upside down in an 890 in gravity, the water in your pool is probably the least of your problems.

Yeah, something for the physics programmers.