If you sent a Pokemon to the Pokewalker, and start a new game to try and get that Pokemon back, the game will not recognize that Pokemon and will not accept it. In fact, it will delete that Pokemon, and will never be able to connect to your DS until it is reset.
People have tried to do this but instead of starting a new game, they instead attempt to clone Pokemon by simply putting a Pokemon in the Pokewalker, and while it is saving when finished transferring, shut off the game before it saves, leaving them two of each Pokemon in the Pokewalker and the game.
But if you try and connect that Pokemon back to the game, the game will (from what l heard somewhere) actually delete both Pokemon.
I'm sure the Pokemon company thinks about these kinds of things beforehand!