The only time any GBA or DS game ever does that is if the cartridge (game pack) itself is damaged.
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make a new file and save it
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on the menu list where it says continue game, down you will find a box that says new game you press it save and press yes and you will delete the other file and have a new file.
Start a new game and when you save it will say that there is another saved file do you wish to replace it? Click A on yes. The other file will not be there but your new one will. Note: You can not have two saved users on Pokemon Emerald or any other game of Pokemon for GBA or GBA SP or Nintendo DS.
you can't