I still have the tape of NYCB's Swan Lake, and I drag it out occasionally, usually turning it off before Act II. As I recall, Martins altered the black and white pas de deux a little, but not substantially. However, Woetzel and Weese's styles of performing them are so strange that I receive the impression that the choreography is entirely different, and he added some annoying complications to the various dances of the swan corps. They also dance the entire ballet practically in fast forward, so many nuances are lost, along with any semblance of plot.
Martins completely re-choreographed the Act I pas de trois, and removed the big swans pas de quatre. The little swans are still there, with small changes. He also altered the ending, which appears to have been stolen from "Giselle"--that is, Odette remains a swan and bourrées offstage, and Albrecht--I mean Siegfried--kneels in grief or something.