Will you automatically switch out or something? sky battles are for flying types, but if you did that your no longer a flying type. . . I forgot about gravity, please include that too.
Gravity Gravity is a prohibited move in Sky Battles. If you try to use it, it will fail.
Roost Roost is absent from the aforementioned list, so logic dictates that you can use it in a Sky Battle.
Most Flying-type Pokémon and Pokémon with the Ability Levitate are eligible for Sky Battles. They do not lose eligibility even if Mega Evolution or a move like Roost or Gastro Acid leaves them exposed to Ground-type moves.
I assume that Roost works like it normally does in a Sky Battle.