There is a procedure to re-sync your Pokewalker with a new save file:
-Go to the Pokewalker menu, where it should say 'Save and go on a stroll'
-On your DS hold the L, X, and Down buttons
A caution chatbox should appear asking if you're OK with deleting the info, as long as you say Yes it should be back to factory settings like before you activated it.
(Almost forgot to add that no Pokemon can be re-obtained from the Pokewalker that's registered to a deleted save file)