Because they've been referred to in that time since. Even still, it makes absolutely no sense why they would destroy some of the highest-quality material for the film--the SE is actually made up of parts of the IN.

I think this whole thing stems from a confusion of a few sources:

1) Lucas says the original print doesn't exist anymore. He's talking about the O-neg. And he's right--its been re-edited into the SE. You'd have to go back to the trim bins and put the original pieces back in.

2)Lucasfilm claims that the GOUT is the highest quality material. This is, frankly, marketing bullshit; its the best pre-existing video transfer, is what they perhaps mean.

3)Lucasfilm indeed took OOT prints out of circulation. Were some of them destroyed? Maybe. After all, what is the point in having 100 degrading, scratchy release-prints of a film that will never supposedly be screened again. They almost assuredly kept a master release print, I'm sure, as this is standard practice, and no doubt a few exist in the Fox vaults too. However, these would not really be used as sources for future releases in the first place so it really doesn't matter.