As I understand it they have all footage, including various unused takes. That's one of the problems, to get HD episodes they would have to check tons of film, pick the right takes and recreate the episodes from scratch, redoing every single effect, not just space scenes, but view screens, transporter effects and every friggin blip that was added in post-production.
I've misunderstood the previous posts. I assumed that some of the original shot film was missing. I knew they'd need to redo all of the effects/comp works from scratch though, and was aware of the huge undertaking to redo the editing. But as long as all of the pieces are there so that it's possible, it will happen some day.
That's the kind of project I would kill to work on. And I know I could do at least as good as the remastered TOS