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In the white tree hollow some of the Pokemon I battle don't register as iv seen them in my pokedex while it seems some do. I can note specifically togekiss. Is this normal?

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Yeah. Totally normal. Pokemon you see on things like the White Treehollow, Battle Subway and Wi-Fi Battles don't register in your Pokedex.

Source: Experience

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Or in online battles it would seem? How does one go about getting something in unova like nincada or togepi or any of their evolutions then? Aside from moving them from like, gen 3 or 4
You have to use GTS Negotiations and hope someone offers you one.
in the global trade it doesn't let you search for pokemon you haven't seen though
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Pokemon that you seen in White Tree Hollow / Black Tower are not registered on the Pokedex.

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