Hmm. Did you upgrade your computer, or change to another machine? Save files go somewhere that you have to go way out of your way to delete. I wish PyTom would add an Uninstall feature that would get rid of your save files along with your game if that’s what you wanted, but nothing like that exists today.
Of course, the game has been improved a lot since the beginning, so maybe you’ll see things on a new playthrough that are better than they used to be?