Unfortunately, you can't; there's a whole thing with dialogue about how they can't once you get every Chaos Emerald.
edit: Unless you use an "all super" mod, but even then it's kinda odd.
It should be possible to use this mod with a previously-started save file. As it is Lua, it only adds its own code and should not modify the game itself in a way that makes the save file unplayable. Unless the mod marks your game as cheated...?
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