Well, the deal is a development deal I think, so they can be moved to other shows if required. That said, I doubt Lost will be goin' anywhere soon.
"Startrek 11" has been formerly announced and a release set to December 2008, with Lost's producers working on it. So Kitsis and Horowitz will come on board next year as producers/show runners during filming of that, I suspect. Could be a good thing, could be a bad thing. Same thing happened during X-Files for the X-Files movie, during exactly the same season as it happens.