The video masters were almost certainly encoded with timecode which links each frame of the master to the exact frame taken from the original negative. It's a relatively simple process, once the original negative has been re-scanned in HD, to use this timecode to exactly recreate the SD edit in HD.
Yes, but it's still a recreation of the original and a complete waste of time. The purists who want the originals preserved and included won't be getting it, and those of us who don't care wouldn't watch it anyway, so it would be a waste of time.
Speaking of the "jarring" transition between HD video and SD visual effects, the visual effects will in the very least be upconverted. Watching the episodes wouldn't be outside of the experience of the new Babylon 5 transfers, which is problematic, but still quite watchable. And, if the film elements of the visual effects are recomposited rather than recreated digitally, they can be seen in true HD in their original form.
If they could indeed do that, it would negate the need to change any FX in the first place, which would for most people negate the need for the "original" episodes to be included alongside the "remastered" episodes.
EDIT: Harvey, you get points for calling Star Trek by its proper name and not "Tee-Oh-Es."