[LigH]

I don't know if the automated tools can handle this. What I know working reliably, is the manual method:

You extract the audio tracks to separate files.
You convert the video in a manual video encoding job via the Queue.
If you want the audio tracks converted too, you also create audio conversion jobs for the Queue.
You use the manual multiplexer tool (in the "Tools" menu) for your desired container (MP4 or MKV, usually, Ctrl+4 or Ctrl+5).
You load the converted video track into the multiplexer window, then you load one audio track after another (may they be original or converted).
You finish the multiplexing job and run it in the Queue.