I think your interpretation of this article's title is wrong. The Library of Congress did not have it's Copyright application prints replaced. The original prints given in the year of the films release are still there.

1977 - Star Wars : http://lccn.loc.gov/96512247
1980 - Empire Strikes Back : http://lccn.loc.gov/96512208
1983 - Return of the Jedi : http://lccn.loc.gov/96501520
1997 - Star Wars A New Hope Special Edition : http://lccn.loc.gov/97510343
1997 - Empire Strikes Back Special Edition : http://lccn.loc.gov/98502262
1997 - Return of the Jedi Special Edition : http://lccn.loc.gov/2006642053
1999 - The Phantom Menace : http://lccn.loc.gov/99468631
2002 - Attack of the Clones : http://lccn.loc.gov/2002636427
2005 - Revenge of the Sith : http://lccn.loc.gov/2005644161
2008 - The Clone Wars : http://lccn.loc.gov/2008636030

It was the copy that was given (maybe) in 1989 as part of the National Film Registry which could have possibly been swapped. But I've been told conflicting reports, A: the swap story and B: the one where they never got a print in the first place.

I need to reach out to them again to find out what happened after ESB was included to the NFR a few years back. Last time I got a reply they had not been given a print, but that was a month or two after the announcement, way too early. Tried a year later but didn't hear back, need to try again.