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Does anyone know how to take a video and re-encode the audio, but just copy the video data using FFMPEG?

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Yes, this is definitely possible to do with ffmpeg with one command, but more information is needed for an exact example. What audio format do you want for the output? Please show some information about your input: ffmpeg -i input.foo –  LordNeckbeard Dec 25 '13 at 8:04
    
Another forgotten question... –  LordNeckbeard Dec 29 '13 at 18:44
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2 Answers

I know that Virtual Dub can do this, but it only works with a limited number of codecs. Since it's free, it's worth a look to see if it'll do what you want.

Otherwise, any demux/remux software will work, but it'll take three steps. First demultiplex the file into video and audio streams, re-encode the audio as needed, then remux them into a combined stream.

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So Apparently FFMPEG can do this, I had to use -c:v copy and that will leave the video stream intact. I actually used an app called iFFMPEG to figure this out.

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Note that if your input contains more than one video stream then only one will be stream copied by default. You can add -map 0:v to include all video streams or simply -map 0 to include all streams regardless of type (video, audio, subtitle, data, etc). See the documentation on stream selection for more info. –  LordNeckbeard Jan 1 at 1:49
    
Thanks, I actually just ran into that. –  Kronusdark Jan 3 at 3:06
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