Well, yeah, sort of. I don't use the avidemux, but would if it would repair that. With mplayer it rebuilds the index to actually correctly seek the movie from a corrupted download.
What you want is for a program to see your movie, go through it bit by bit, compare what is missing to a database somewhere, plug in the missing info, rebuild the index, and then output to overwrite the file. I highly doubt you'd find something like that
Best bet is to remove the garbage, rebuild the index, and then watch the movie with the small bits missing.