Ingrain causes the Pokemon to use the move to become rooted firmly to the ground. If said Pokemon is Flying-type, has the ability Levitate, or is under the effect of Magnet Rise/Telekinesis the Pokemon will leave the air and become rooted to the ground by the means of the roots it has sprouted.
I'm guessing you mean Latias' used "Telekinesis" in which case the move will fail because then the Pokemon would have to not only move the opponent's Pokemon off the ground, but all the roots that are deeply interwoven into the ground.
I suppose through anime-logic it could work though the Pokemon in question using the move would have to be an extraordinary Physic-type user such as Alakazam or Mewtwo.
