Hello. The saves should be in a "save" folder in the same directory from which you run your game. The achievements should be in "user/game_data.json" along with other data.
Could you check if you still physically have those files on your system (especially the save files) and they're in the same place as the game? I don't know what could be deleting them, the game doesn't try to delete anything. Maybe the operating system is not allowing it to read files for some reason.