The thing is that a lot of the SE changes were made in 2004. That means they are hardwired right into the Lowry transfer, so to speak. That was one reason why they re-used the transfer for the blu-ray, and I am guessing the 3D releases as well. There basically is no more "negative" of the SE, it's all digital now because the 2004 changes were never put on film in the first place.

When it comes to an eventual OOT release, I predict they will either use an early generation archival print master and restore it, or base it off the negative. Obviously there will be a lot of challenges with using negative because so much of it is the SE; they'd have to fill in the holes using another source and then somehow match them together. Personally, I don't trust them to do it right. A lot of the SE changes are so subtle that they might overlook them or just leave them in. Stuff like the re-comps. They might not see the point. That's why I hope they just go get the best non-o-neg print that exists and clean it up, the negative has just been too reworked. That might be seen as lazy by some, and creating a poor quality scan by others, so I'm not sure what they will actually do. Probably they will use the negative and fill in the holes, but probably they will accidentally leave some changes in the film. The amount of work they will do will depend on how big of an 'event' they want to make the release.