Say, you have processed some video container. Now it has no sound.
The solution is simple: supply two inputs into commandline ffmpeg utility and map channels accordingly:
ffmpeg -i processed.mp4 -i source.mp4 -map 0:v:0 -map 1:a:0 processed_with_sound.mp4
UNDONE: treat all other command-line options as key=value pairs to feed into the output AVCodecContext instance.
UNDONE: write me!