PokéBase - Pokémon Q&A
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Let's say you caught all Pokemon and used 4 pokeballs, do your other 3 balls get thrown away along with the Pokémon ?

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Yes they do. If you choose to keep a Pokemon you caught, you take that one and the others simply go away with the Pokeballs you caught in. Choose wisely: I recommend you take the legendary. If you have already caught it in a previous trip, take one that isn't in your Pokedex.

Hope I helped!

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Merci =)