If your path is closed, then you can go to the "align stroke" portion of the stroke pane, and tell Illustrator to put the stroke inside of the path rather than along it. Or outside of it.
Though I'm not completely sure this is the problem you're having - you change the stroke to a high value, then change it back, and the underlying path is distorted? I've never had that happen in the decade I've been using Illustrator. What are you trying to accomplish here?