I remember doing an intense reread of Proven Guilty to try and determine what exactly happened in that book without referring to other books in the series. And the most obvious answer for who fixed Little Chicago is...
Harry himself. I submit that Harry at some point gets unstuck in time. He skirts the no time travel law by mentally time traveling, a la Billy Pilgrim from Slaughterhouse Five or Desmond from Lost.
Early in the novel, Harry makes a big deal about how realistic Lash's illusions are, and then promptly gets hit by a mysterious car. This was an illusion because Future Harry made an ally of Lash, and they used the ensuing concussion to hide Future Harry as a ridealong in PG Harry's skull.
Bob and Harry also discuss time travel at length because of the future info that Rashid passes on to Harry. We never find out what this future info is it anything about it. I suspect this is also Future Harry ensuring that PG happens the way it's supposed to.
Finally, Little Chicago. Future Harry fixed it. Any questions?