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Don't think AVI (and therefore AVS) generally support more than 1 audio stream, so the problem does not often arise.
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Yep, you're right, Avisynth always outputs a single audio stream of x channels, which is why whenever I have two languages (like CH.1-2 Stereo Full Mix German - CH.3-4 Stereo Full Mix English) I index them both, then use MergeChannels to make a single audio stream with 4 channels and then I specify how to divide them and encode them separately to the encoder.