You should be able to just "remux" the file.
Say you have a file with 1 video stream and 1 audio stream. You can do
Code:
ffmpeg -i bad-video.flv -c copy good-video.flv
If indeed you need to do it in 2 steps you can do this
Code:
ffmpeg -i bad-video.flv -map a -c copy astream.mp3
ffmpeg -i bad-video.flv -map v -c copy vstream.flv
ffmpeg -i vstream.flv -i astream.mp3 -c copy good-video.flv