I know that Phantom Hourglass had two. I think Spirit Tracks might have but I am not quite sure.
You have saved me from having to dig through a bunch of boxes!
That’s the thing, I can’t remember if it was Spirit Tracks or Phantom Hourglass or if there even was one with 2 save files (besides MM) to begin with. I guess I’ll just have to dig out my copies from… wherever it is I put them lol.