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i'm sure there's an easier way to do it, but what has worked for me in the past has been to encode the avi as vob, then use vobedit to separate the audio from the video. do that with both avi's, then import the audio from one to the other. after that, i would recode the vobs back to an avi.
prolly more steps than you need, but doing it this way allowed me to mess with the audio before merging with the second vob. i've mentioned adobe audition in threads before, but i just can't say enough good things about it.
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