You cannot regenerate Legendary Pokémon in Pokémon Diamond. The regeneration feature for Legendary Pokémon was created as of Pokémon Platinum so it is not available in Diamond so for Legendary Pokémon in Diamond, you will have to get any of the Legendaries that you have knocked out from another game however you can save before challenging the Pokémon so if you knock it out, you can just turn off your DS and turn it back on so it'd be before you challenged the Pokémon.
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Empoleon is not a legendary Pokemon. It is the final evolution of Piplup, one of the starter Pokemon in Pokemon Diamond, Pearl, and Platinum.
capture the legendary and train your Pokemon
when you get your seventh badge and you will head for mount cornet
you can go after the legendary pokemon, or beat him again.