I’m aware of the clean up that happened in the 90s, because the film was in bad shape. So as far as I understand things, the original negatives were scanned digitally, cleaned up, and then used as the basis for the special editions as well as the 1993 release.
The 1993 release was simply the final time a fresh video master was made from the 1985 interpositives (it was done for the definitive collection laserdisc release in '93 and reused for the “Faces” aka “One Last Time” aka “THX” release in '95). Since it was still the early 90’s, this last video master was only done as a 4:3 standard def transfer with the 2.35:1 image letterboxed. Hence, in 2006 when George was reminded by the people at Lucasfilm that an unaltered dvd release would make quite a bit of money but he didn’t feel like spending a dime on it, this was the most recent transfer and we got the GOUT.
The restoration for the Special Edition wasn’t even started until 1994 and involved physically cleaning and restoring the original negatives themselves. No digital scanning was done except for the SE additions where cgi was integrated into existing shots. The technology to digitally clean up an entire film at resolutions high enough to be printed back to film for theatrical exhibition wouldn’t exist for another several years AFAIK.
The SE restoration is a fascinating subject in and of itself since they cleaned the entirety of the movies, including the parts that were going to be replaced anyway for the SE. Some frames on the o-neg were damaged beyond repair and were replaced with dupe neg made from the '85 interpositives since that was the next best source. So not only are the altered parts of the negative still in storage somewhere, the '85 interpositive is also a viable source for an OOT restoration should it come to that.
But yeah, what Density said x1,000,000. See: just about any criterion release for good examples of stunning restorations that didn’t use an original negative.