I can't recall if it did with 1.0 to now. If you have the physical disk, you can test it. Uninstall, reinstall, start a game, save, update, try to play the same game.
As a note, the patches for Gal Civ 2 did cause saves to break, if I remember correctly. So, though they are different developers, it might be the same here due to Stardock Central.