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Once a Pokemon is inside a Pokeball, no matter what type of ball it is, the ball is permanently used. Say you migrate a Pokemon from Emerald into Diamond, the Master Ball will disappear and will be replaced with the special Pokeball used in the Pal Park. The only way I can think of you getting that Master Ball is using a GameShark or Action Replay code, but that code has yet to be made.

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Q: Can you get a empty masterball if a Pokemon is inside it in Pokemon emerald?
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What if Stevens house is empty Pokemon emerald?

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