PokéBase - Pokémon Q&A
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I had an epic fail in Pokemon Heartgold by defeating most of the legendaries...

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Lugia
Ho-oh
Suicune
Zapdos
Moltres
Articuno
Mewtwo
Kyorge
Rayquaza (Only if you obtain both Kyorge and groudon; groudon is exclusive to soul silver)
Dialga, Palkia, Giratina ( Only with the event Arceus)
Latios, and latias (Only with the enigma stone wifi event)

The amount of times to rebattle these Pokemon is unlimited as long as the elite 4 and champion are beaten after they faint. Upon capture they will not appear for battle.

Source: Serebii

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Thanks! Also, could you please put how many times you can rebattle them?