It was mentioned on the official Star Wars site back in 1997 that before any alterations could be made, they had to make a restored unaltered print first. I can't imagine why you would then cut up that reel instead of make a duplicate first. Lucas didn't know exactly what he would change. There was an article about how redoing one of the Death Star battle shots would make other ones look dated. So they would redo more. And there are the shots that used original footage with CG added. Lucas might have thought in another 20 years he may want to redo some of the CGI so that be easier if he was sure to save an unaltered print.
Like when Jabba was redone in ANH in '04, did they go back to a print with just Mulholland in it and make a new Jabba or just paste it over the '97 one? Some of the CU frames of Han Solo that were cut out in the Greedo scene to make way for the overhead shot were reinserted back in for the dvd. The words "Yes" and "I" were put back to "bet you have."
(The '97 Greedo scene can be found on the deleted scenes video of the Episode I dvd if you want to check)

So don't tell me Lucas can't restore footage that was removed in '97, he already did. I just wish there was an easier way to show or explain this.