So you're telling me that the last time you played you had the official version, not some modded/compressed version, then now you again got the official version and the saves are not compatible? Not a single save is compatible and you have to restart the game.
It's impossible! The game is made in a way that if you don't mess up with the scripts, it will always know where to continue from. Even if you make a save on the last screen the one with "Coming soon" and you load from there it should still work.
For the saves to no longer be compatible it would mean that the game is trying to load the game from a point that is no longer in the script and I never removed any lines.