The original question, regarding going back and 'finding' the film footage, isn't outside the realms of possibility.
The Seinfeld DVDs were, to my knowledge, produced in that fashion. That went back to the masters and re-edited everything anew to the exact frame. Now, Trek also has the effects to worry about, but the fact that the original film is presumably still good to go, we may see them redone "some day".
I'm not holding my breath, but a man can dream.
Remastering aside, I'd kill just for DVDs that didn't look like smeared crap half the time. TNG and (even moreso) DS9 really suffers due to porr compression.