Board Thread:Lore Discussion/@comment-10561605-20130820164006/@comment-112.198.118.10-20160515112336

Anyway, I've heard that Alduin is actually a godling, and his dragon form is just that, a form. He isn't actually a dragon, like how a dolphin isnt a fish despite looking like one. So his soul wasn't absorbed. Maybe he was possessing a dragon, and so that's what was absorbed when the Dovahkiin killed his mortal body.

Alduin's souls was not absorbed because he is still the world eater, and will return to fulfill his role when the time comes, according to Arngeir that is.