@Siphonay the pokewalker routes you have unlocked are stored in the game's save data and the pokemon you sent to the pokewalker is also stored in the game's save data. You can change the game the pokewalker is paired to, but you need to reset the pokewalker each time you do it (you will lose ansynced data in the pokewalker, like items, caught pokemon and steps). If you forget to send back your pokemon to the game after resetting the pokewalker, you can recover it via the pokewalker menu of the game.