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Yes, the new moves that they learn will replace the move at the bottom of their move list. To change that move, go to your Party, click the Pokemon then click summary. Somewhere it will show it's moves. Press the move at the bottom and press switch. Then click the move you don't mind losing. Now, when your Pokemon learns a new move in the daycare, it will replace the move you don't mind losing. Awesome huh?

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