I would think they would take the stems (dialogue, stereo music, sound effects) that they used in 2002 to remix the sound to 5.1 for the DVD release now and remix it to 7.1 for the Blu-ray release.Regarding the audio, they've stated it's being mixed for 7.1 surround, but I haven't heard how exactly they're doing it. I would imagine that if they're completely recompositing the sound they'd have made a bigger deal about it. My guess is they're using the 5.1, remixing it and tweaking it as needed
They either are doing it from the stems for all episodes or doing a matrixing software taking the 5.1 mix from 2002 and making it 7.1.
For any special episodes they might extend they would have to remix any specific scenes in 7.1 from the stems and that would also entail a lot more work. See this thread:
Measure of a man - extended version on blueray
for a possible but unannounced season 2 special feature if they go back to the camera negative to create this. They would have to go back to the 1/4" analog audio reels of production sound and possibly place new sound FX and ambiences, and possible unused music cues. Since it is unofficial please direct any comments you have for that episode on that thread.
If any other episodes did an extended version the same level of audio work would apply. I would love to see them dive into the audio archive for computer voice and the use of a possible database library from Majel Barrett of words and syllables, vowel sounds to create a computer voice sampling for a future Trek series and Star Trek XIII. See this post .
http://www.trekbbs.com/showthread.php?t=77868&highlight=voice