Good luck on the DDS conversion. I have had to do multiple save/re-saves to get things done just right.
To point out: While "Their Finest Hour" and "Flaming Sword" are renamed filename wise to remove them from the actual campaign pool, and while they are not the original "V" missions, they exist because they follow the spirit of our perceptions of the way it maybe might have been. Granted, these are the only two possible mission exceptions that I've ever seen, but they do exist.
"Flaming Sword" more than anything raises the point I want to make: the Astaroths are turned into Mara's in the "fixed" version, but turning two herc's into loki's is unacceptable? For all we know, the hercs were a simple fred mistake. Considering the deliberation of time that it takes for the audio files to be created, I find that a more plausible explination.
Can we atleast (or may I post) the alternative mission with that change for others to put to question if it unbalances things? Or at least a definitive statement (additional or otherwise) that states that it does categorically break something?