Bad news.
Robert Harris recently said words to the effect of, "I'm not worried about Lucas' crusade, because I know the films are preserved. No matter how much time goes by, when the go-ahead is issued to transfer the films it doesn't matter what state the negative is in." He was referring, I think, to the fact that there were 3-strip dupes.
But, I think in ILM:Into the Digital Realm it states that they used some of the 3-strip sources for ANH:SE, so now I don't know what to think. You could digitally re-sync one of the layers, as Harris said he had developed his own methodology for re-constructing 3-strip dupes. I think it's common for 3-strip dupes to have one layer or more out of sync because of shrinking and swelling that is common in old films. In 1995, maybe it was impossible to fix but hopefully now it is.
Risky business in any case...