I can offer some input here. Mainly with regard to the 2004 clip:
-It's not a cleaned up VHS copy. That is absurd.
-It sure doesn't look like a 35mm or 16mm print duplicate of a 16mm negative of a 20-year-old fan-film. Were that the case, contrast would be jacked way up, there would be lots of grain, as well as ample amounts of dirt and scratches, and you wouldn't have as much detail as the clip shows.
So, what does it look like? A scan of the negative. I'm telling you, that's what it is, nothing else makes sense.
When Davis says the negative is "lost"...
-does that mean he lost it himself, or Lucasfilm does? Who owns it? My impression was that Lucasfilm does. If they don't, they probably made a duplicate negative for their archives. But I believe they always had the only existing print copy(ies), and that they gave Davis a VHS for him to watch, which he has held on to and toured around since then.
-When Lucasfilm told him "it's lost", what does this mean? It means they just couldn't find it. This was shot in 1982, they made a VHS copy for Davis to keep and then filed the negatives in the archives. Who knows where they went, little dinky miscellaneous footage like this might not have even been properly catalogued, since it's not actual dailies. "Lost" doesn't mean "gone," it just means Lucasfilm isn't going to hire a film librarian to spend three months searching the unordered/mislabelled footage in the archives to the tune of a few thousand dollars just so Warwick Davis can show a 10 minute clip at conventions.
Lucasfilm hires a film librarian to comb through the archives for the 2004 DVD, looking at raw dailies, outtakes, perhaps even unprinted takes, and all the behind-the-scenes footage (some looks like it is from the raw 16mm footage) they could find. The probably opened up a lot of cans and found stuff they weren't expecting to find. And they had the luxury of doing so because this was a multi-milion dollar project for a DVD release that sold $100 million in its first day of release. And low and behold--a scan of the Return of the Ewok negative, or some sort of print master, appears.
Now, why didn't Hyperspace use this and have to ask Davis? 1) Maybe departments at Lucasfilm don't talk to each other. This is a huge issue in major multi-division mega-coporations, and one of the reasons Lucasfilm wanted to move to the Presidio complex. 2) Maybe the web people didn't know about the 2004 footage. 3) Maybe they knew, and when they realized it would cost $20,000 to scan the negative for a website freebie that isn't even the full film and is small resolution--they asked Davis for his VHS instead.
But based on the sheer fact that the 2004 clip exists, I would say Lucasfilm had the negative the whole time ("it's lost"--in other words, we just can't find it by looking up the catalog), and found it when making the 2004 DVD.
Does Davis even know about that footage? If so, what does he think?