PokéBase - Pokémon Q&A
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Just defeat the elite four and he will respawn, but of course you will still have to meet the requirements of him appearing (You need to have a Pokemon at lvl100 on your team while you soar with Latios or Latias).

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All of those requirements are met and I defeated it, but  it takes forever to come back
Try waiting a day after you have defeated the elite four and if that doesn't work then I'm stumped and I'll hide my answer.
I went back every day and it still hasn't shown itself except on certain days