To load the audio, it depends on the audio configuration . You have to load each track with FFAudioSource, and specify the track number. You can use mergechannels() to send them or you might want to down mix them to stereo since it looks like you're using 2ch aac
For example 4channel mono
Code:
FFVideoSource("blah.mxf")
#whatever video filters here, depan etc...
vid=last
aud1=FFAudioSource("blah.mxf", track=1)
aud2=FFAudioSource("blah.mxf", track=2)
aud3=FFAudioSource("blah.mxf", track=3)
aud4=FFAudioSource("blah.mxf", track=4)
aud=mergechannels(aud1,aud2,aud3,aud4)
audiodub(vid,aud)
If you send 4ch in the avs script, you can also use -map in ffmepg to select specific channels
Yes, it's possible to do recursive subfolders with ffmpeg batch . There are some examples posted at videohelp.com and I think here too