The process of making a Pokémon battle-ready deletes its record of relearnable moves (if any, excluding TR-taught moves) and replaces its current move set with level-up moves, ensuring that the Pokémon cannot know any moves it could only learn from a previous generation.
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This means that the NPC deletes all moves the Pokemon has, regardless of what they are, and replaces them with the level up moveset your Pokemon would have if it was caught in the wild at your Pokemon's level.
