Probably not. For security reasons Javascript tends to limit access to various things, otherwise the web would be full of dodgy scripts which changed all sorts of things. Javascript is very sandboxed.
I don't quite see why you'd want to. Your 5 JSON files are your games initial state, and your localstorage version is the current state of the game. Overwriting your original files sounds like a bad idea - supposing you wanted to restart the whole game, where would you get your original data from.
More to the point, does it *matter* ? JSON files, even quite complicated ones, take up very little space compared to sound or graphics files.