PokéBase - Pokémon Q&A
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After receiving Shaymin in Pokemon X AND getting Shaymin's respected Gracidea to change it from Land to Sky form, I've noticed that Shaymin changes back on its own! AND, when I try to use the Gracidea on Shaymin again, it says "It won't have any effect" so I'm wondering if there's a timer and cooldown for the Gracidea

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Shaymin changes back to Land Forme during the night, if it is frozen, when deposited into the PC (prior to Generation VII), when withdrawn from the PC (Generation VII), when deposited into Pokémon Bank, or when deposited in Pokémon Day Care or the Pokémon Nursery.
When used from the Bag on a Land Forme Shaymin, the Gracidea changes it into Sky Forme. It cannot be used at night or on a frozen Shaymin.

Source- Bulbapedia

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