"/setparty <level> ["moves"]: This command will permanently set the levels of all of the Pokémon in the player's party to the specified level. Adding the "moves" argument to /setparty will prompt the player to choose up to four moves from each Pokémon's level up movepool up to the specified level. If no moves are chosen for a Pokémon, the Pokémon's moves will be randomized. It is not possible to retain the moves that the Pokémon initially had."
-Straight from our Wiki, http://pixelmonmod.com/wiki/index.php?title=Commands
What would be good, is allowing an option to retain the moves. Then again, the first command, /pokeedit, does that for you. You can also use the in-game wand to edit pokemon.