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.