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http://www.bttf.com/forreal.htm

"Which brings us to an interesting diversion... keep in mind that the filmmakers really did go back in time when they went back to the same locations to shoot the film all over again. As everyone has heard, Back to the Future was actually filmed twice—once with Eric Stoltz in the role of Marty McFly, and once with Michael J. Fox. But despite Studio proclamations that only a few scenes were involved, the truth is that the majority of the film was shot with Eric Stoltz. At each location we visited, we spoke to the folks we ran into (OK, so we don't follow our own rules!) and each of them confirmed that filming did, indeed, take place twice.
It seems that the young Mr. Stoltz, a fine and serious actor, was coming off a little bit too serious, especially in his scenes with Doc Brown. Through no one's fault, the all-important and all too rare chemistry between the two lead actors just wasn't working. So Bob Zemeckis, demonstrating the tremendous dedication to his art that has become so apparent in years since, asked Steven Spielberg if he could recast the film and reshoot the Marty McFly scenes. Obviously, the answer was yes...meaning that every scene that featured Eric Stoltz on screen had to be reshot. (Well, almost every scene. There are still a few shots lingering in the film that are clearly not Michael J. Fox! Keep that freeze frame remote handy!)"