Again, this isn't so much a matter of changing things as a matter of ugrading the resolution. The Deep Space Nine effects were produced on video, at 480p. The show was, of course, shot on film, which is many times the resolution of HD (1080p). However, in order for everything to look right on HD the effects will have to, in the very least, be re-rendered in the higher resolution of 1080p.
Not that I wouldn't mind What You Leave Behind, as well as the last episode with Kor, seeing some major changes. But I could live with both if they didn't.