Defeating Kyogre in Pokémon Sapphire and Pokémon Emerald will mean that it will not return however it will return if you defeated it in Pokémon HeartGold. In Pokémon HeartGold, there's a regeneration system that will regenerate all 1-off Pokémon such as Kyogre, Entei, Suicune and Raikou after defeating Lance.
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you have a new Kyogre and become epic, congratulations!
Go on to defeat the seventh gym in Mossdeep City, if you did not already catch Kyogre.
It will come and kill you in your sleep. Goodnight
Go defeat the elite four again and all non caught legendary Pokemon reset
You'll have to go into the cave that is just north of them and defeat team Magma/Aqua. Then you might have to fight Groudon/Kyogre. After that they should have moved.