I don't know how the original negatives are stored - are they cut and then comped on video, or the entire episodes shoot is scanned to video and then cut and edited?
Back in the 90’s the original film was processed to allow for positives to be made and then it was the positives that were actually telecined to videotape; the film then went to the vault.. If it was just a live-action scene, it went to both VHS and D2 composite tape (the VHS was used for the cheaper offline edits that allowed for the editor edit different cuts together before the final edit was done on the higher, more expensive D2), while special effects and model shots went to D1 component so that the effects house could compile the shots in higher quality component, and then the completed effects shots were transferred to D2 for the editors at Paramount to edit into the episode master.
The original 35mm film was kept in a salt cave for TNG, and re scanned for the Blu Ray. I think DS9 is the same, but CGI assets are separate and many would be missing.
I wish people would actually look things up before speculating on the whereabouts of the DS9 CGI assets. Few, if any, of the CG assets are missing. The DS9 CG models are the source (or at least the starting point) for a large chunk of the Eaglemoss ship collection. There's been demo still renders floating around online for years. Most of the textures are 2048x2048, which was way overkill for the time and sufficient for 1080p if not 4K now.
Nope. The whole point of these systems are to fill in missing data points in images. Subpixel data can be recovered temporally (reviewing several adjacent frames), predictively (half a face gives enough details to figure out the rest because faces ain't that different) or reconstructively (building a catalog of people, props and sets and figuring out when each person or item is in a frame and using close-ups from an entirely different episode to fill in detail). All of these methods are in use now. They are not likely to be ready for something like a DS9 remaster...yet. Someone out there is probably writing a PhD thesis on how to do it as I type here. "AI" gets a lot of hype these days, much of it overblown, but the tech can do image processing. Image processing is precisely how self-driving cars operate.
Not to mention, but the whole “Ships Of The Line” Calendar Line was started because of the opening shot in the Voyager episode “Relativity”. And the CGI models for Voyager and DS9 have been used for it.
Indeed, and if I remember correctly, this short video was done by one of the VFX artists who worked on DS9, using the original CG elements, to show-off how the DS9 CGI would look at full HD: EDIT: he also did this jaw-droppingly gorgeous video of the Ent-E that I seriously cannot believe it's all CGI. The dude is good.
Man, that 1701-E lounge is great. Never even thought about how (unlike the D) you'd see a lot of the ship out the back.