Cynthia is not the champion in the johto region in Pokemon heartgold,you can't find her in it, but she is the champion in Pokemon pearl,diamond, and platinum versin and that is the sinnoh region.
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You must have the event Arceus and go to the Ruins of Alph.There you will find Cynthia and she will give you Palkia,Dialga,or Giratina with their orbs at level 1.
You can find it in Pokemon Platinum, Pokemon Crystal, Pokemon HeartGold, and Pokemon SoulSilver.
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You can only find Skarmory in the Pokemon SoulSilver version.
you can find her in the elite four thanks