User blog comment:JAlbor/Assassin's Creed: Black Flag Q&A Opportunity/@comment-6517-20130812123702/@comment-13471981-20130813104431

Personally, I think he was deleted. There's not really been any indication that Clay lives on in Desmond in some way, and even if there was, Desmond's dead now, so... :/

But I'd love confirmation for this, so if the Wikia Contributor could provide a source, that'd be wonderful.