Say a player announced "double Afterburner" for his two Typhlosions in play. However his Discard Pile only has one Fire Energy card for him to use. Does that mean his second "Afterburner" Poke-POWER is used up, or can he use it later in the turn since nothing happened for the second one?

Since you cannot use an Ability for no effect, if the player only has one Fire Energy card in the Discard Pile the first Afterburner Poke-POWER may be used but the second cannot. So since it is not used up the player could use the second one later during the turn if a Fire Energy card somehow ends up in the Discard Pile.

Relevant cards

HSP_HGSS09