Encoder not reading audio channels

Hi All,  a question about audio channels...

So if I have a Quicktime video with audio on channels 3&4 (but not 1&2) Encoder ignores the audio completely. I have ProRes recordings on an Atomos device that can record up to 8 audio chanels and can assign embedded audio to any of those channels. If I choose to input analogue sound it is prioritised on channels 1&2 so embedded sound is pushed to 3&4. Are there settings in Encoder where I can tell it to encode channels 3&4 to the output?

There is probably a sensible explanation, I just can't think of it

Thank you in advance