Pokemon would count as pets, aside from specific Pokemon that have enough of a personality to be considered appable themselves (ie Meowth and Mewtwo). If a trainer has the pokeball with a certain Pokemon in it on their person (pockets or attached to their clothes), they would be able to bring it along. Otherwise, yes, they can be regained. It would be considered a small object regain (except in the cases of large Pokemon like Wailord or Gyrados).