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Avidemux can only handle one audio track internally.
Nonetheless, there is a way to add a second audio track, with limited support and no processing at all on that second audio track.
The second audio track must be CBR, that is MP3 CBR or AC3. It only works when the output format is “AVI, dual audio”.
To add a second audio track, use the Audio→Second Track menu item. After selecting it, set the output format to “AVI, dual audio”.