I apologize if this question has been answered already. I did a search and didn't find anything relevant, so I'm sharing my experience in case anyone else runs into this issue.
I recently shot a multi cam interview on two 7D's and one HVX200A (in fact, I do this fairly regularly). Usually when I capture the HVX200A footage, I assign channels 3 and 4 as a stereo track, and leave 1 and 2 as mono tracks. This works great, as it allows me to control the stereo mic as a stereo mic, and leaves the mono sources mono.
Since I'm shooting the 7D's at 1080 and the HVX at 720, I then upconvert the HVX footage using compressor so that I can then put them all into one multiclip. However, when I do that, it tends to assign the mono clips (1 and 2) to be a stereo pair, and the stereo mic (3 and 4) become two mono sources.
Previously, I had captured the HVX footage as 4 mono sources and so did not have this problem when multiclipping, and so in an attempt to address this new issue, I then went back and recaptured the HVX footage as 4 mono sources, then upconverted the new clip in compressor, and then made a new multiclip with this new clip, and It has the same problem (though this time, clips 1 and 2 are panned center, even though they are still a stereo clip).
Here is my solution:
I opened the multi clip, selected the audio from the HVX200A, then dropped the multi clip into a sequence. Then I selected tracks 1 and 2 and unchecked "Stereo Pair" in the "Modify" Menu (or Alt + L). I then dragged the multiclip back to the bin and deleted the original clip. From now on, the multi clip is 4 mono tracks. I'm sure this solution would also work in reverse if needed.