I am using the itch.io desktop app to run the Helium Rain launcher exe file. I closed out of my first session from the GUI -- I didn't use alt + f4 or anything -- so it's not like I closed the game while it was still saving.
This isn't caused by a save problem, the static game data was corrupted somehow - the game itself can't do that, as it never writes to that file in the first place. It may be an itch bug, or a hard drive failure. You should try reinstalling the game.