Redoing the 60's FX work, (some of which did win an emmy or two) has been very controversial in fan circles ever since some now defunct CGI fx house proposed it to Paramount almost a decade ago. They redid a couple scenes from "The Doomsday Machine" episode as a proof of concept. A bit creaky by today's standard, but the idea never totally went away. And of course, fan films like "Starship Exeter" have great effects shots now. (Paramount ought to hire those guys!)
It will be a miracle if every film and sound element from TNG, DS9, and Voyager was saved over the years.