What exactly does it mean for the negative to be disassembled?
The first thing they did for the Special Edition was clean up the original negative shot by shot and frame by frame. This process was started in 1994. The technology to do this digitally didn’t exist yet, as it would by 2004, so they were still doing this photochemically. Because the o-neg was made up of four different kinds of film stocks (one for the shots that would’ve come straight from the camera, another for the vfx shots, etc), it had to be disassembled in order to clean and chemically treat each shot with the tender love and care it needed. I’m not sure if this necessitated separating each and every shot (for example, the scene where Luke has dinner with Owen and Beru was presumably all shot on the same film stock, so maybe they were able to clean/bath that scene without disassembling it).
While they were doing this, they also redid the optical wipes. This would have involved separating the end of each scene from the beginning of the next.
The negative has been conformed to the SE since 1997. George decided to cut the changes directly into the negative because, as far as he was concerned, the SE was the official version of the movie now.
We recently got confirmation from the relevant person at Fox that the pieces of the negative replaced for the SE were indeed put into storage and not discarded. It’s worth noting, though, that many of the vfx shots had deteriorated by '97 because of the chemical properties of the specific film stock they were finished on. As a result, even the shots that weren’t completely redone with cgi still had to be replaced. Because the only alternative was going to a grainier second-generation source like an IP or sep, George instead had ILM go back to what I presume were the VistaVision originals (which I guess hadn’t faded as badly?) and recomposite those shots digitally.
I think I remember reading on zombie’s website that the negative need not be disassembled to reconstruct the unaltered version. Because a modern restoration would be done digitally anyway, they would simply need to take a scan of the o-neg as it is now, scan in the pieces that got replaced, and rebuild everything in the digital realm.