I'm not techie, so someone else can help you with the save-files, I hope

But as a matter of achievements : When you have played through the whole game, the 'level select' option will unlock- and you can go back into the game at many points, to replay specific parts and, for example, collect any missing collectibles, smash more stone 'pillars', or whatever you're still missing in the game.

So maybe you don't need to delete anything? But just play on now, and go back to it later...