Re: STID and the Eugenics Wars books
He only calls himself "Khan" in the movie. I'm not so sure they didn't leave themselves some wiggle room on whether Harrison is really Khan.
I know the intent is that he is Khan. But if they decide to use Khan again for whatever reason and Cumberbatch decides to not come back, they can always say he was an Augment named John Harrison who used Khan's identity.
"If we're going to be damned, let's be damned for what we really are." - Jean-Luc Picard, "Encounter at Farpoint"