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.
For this reason, the "inevitable discrepencies" you envision simply won't occur. And, even if the HD edits had to be created by hand, you greatly underestimate the skill and precision of professional editors.
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.