Most of the BTTF fanfic stories would likely end up
getting jossed.
Granted, most of us tend to disregard The Ride and The Animated Seres as a canonical extension of the BTTF Trilogy - but that's because Robert Zemeckis wasn't involved in either. If both Bobs filmed a BTTF4, there would almost be an obligation to accept that movie as a canonical extension of the trilogy.
On another note, there doesn't seem to be a lot of Family Ties fanfic - but anybody who wrote about what happened to Alex P Keaton after the end of the Family Ties series before the airing of Mike's Goodbye on Spin City might end up having their fics jossed by that episode. Not much was really mentioned about Alex P Keaton, though, other than him being a Republican Junior Senator in Ohio - some some may not even accept that as part of Family Ties canon.
BTW, I wonder if anybody wrote BTTF fanfic between 1985 and 1989 - before the sequels were filmed! Flaming Trails has written a few fics as if the events of the sequels have never taken place - but she's still incorporated certain aspects of the sequels into her stories (things like Needles, Hilldale, Clayton Ravine, and Marty's "chicken" problem).