Strip second layer of dual audio for conversion?

[Munus]

Hey guys, i got a heap of anime I'm wanting to convert for my ipod, however the Japanese part of the audio is listed first. The english one is second. This means that when i convert it strips the english audio so only the Japanese is left.

What is the easiest way to change this so when i convert i can keep the english dub.

Thanks

 

[Munus]

Sorry to dig this back up, but im still looking for an answer
Thanks