I have native MXF files from my Canon XF300 machine. During production, we use the two separate audio channels with the intention of keeping them separate for use in the edit. (One of the channels was for boom mic, the other was a radio mic)

When I use HDlink to convert from MXF to AVI or MOV, it appears to downmix the seperate audio channels into one. I can't seem to find any options in the preferences to keep these audio channels separate. Am I missing something?

Surely there should be an option somewhere for keeping the channels separate? Thank you.

That's odd. I do exactly the same thing with a Canon XF300 and (yesterday) camera-mounted mic on Ch1 and boom on 2. They remain separate on the avi files converted through HDLink (can be double-sure, because there's nothing on Ch2 when no boom-mic was plugged in).

(Edit)
Although (thinking about it later) the channels do appear in a single stereo track, which may be what you mean. But, Left (1) and Right (2) are not "mixed", they're completely separate and can be treated separately.