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This came up in an Eldar vs. Tyranids game. My opponent wanted to shoot with his tyrant (using Warp Blast) at my falcon containing warp spiders. He asked me if he could, theoretically, in one turn destroy the falcon in the shooting phase and assault the warp spiders (now disembarked) in the assault phase. Then I realized I didn't know the answer to that. I assume that you could do that with a wave serpent and its passengers because the serpent is an addition to the unit, not a separate choice, whereas the falcon counts as Heavy Support and the spiders as Elites. So, can you shoot at a transport and then assault the disembarked passengers of that same transport? Does it make a difference if they are separate choices in the army (and therefore, might count as separate units)?
"We await the return of the gods as Dyannartan waited for Isha. We die for the Eldar as Dyannartan died for the Eldar. Her deeds in the face of The Great Enemy will ne'er be forgotten as long as we draw breath. Her patience and sacrifice are the devotion of the Protected Ones; the Dael-Durien."
Short Answer: No, he may not.
Long Answer: They are two different units. While the Transport may be attached to the squad, it's considered a completely seperate entity from the unit once the game starts. For example, if you shot at the Warp Spiders, then do any excess wounds carry over to the Transport? Of course not.