Didn't Alias do a major retooling during the middle of its second season, even airing a sort of "second pilot" after the Super Bowl? Sounds kind of similar.
Yes. Midway through the 2nd season of
Alias, SD6 was destroyed and they completely dropped the double agent angle. The show became a more straightforward show about Sydney working as a secret agent for the CIA. Although, rather than drop the SD6 characters, the more likable ones were pardoned and integrated into the new CIA team.
This isn't the first time I've heard of a show getting revamped like this but it is one of the few times I've heard of it getting revamped this early. (The other major instances I can think of were...
Angel Season 5 when they stopped running a paranormal private detective agency and began running the L.A. branch of Wolfram & Hart.
Earth: Final Conflict Season 5 when the Taelons & Jaridians died out, Liam Kincaid died, and the show was now about Renee Palmer & J Street fighting a secret war against a new hybrid race called the Atavus.
Stargate SG-1 Season 9 when Jack O'Neill left the show, Col. Mitchell & General Landry were added to the cast, and the Goa'uld were replaced by the Ori as the show's main villains.
The earliest revamp I can think of is
Tru Calling, which changed the tone of the show significantly halfway through Season 1 when they added Jack Harper to the cast.