I have the exact same problem. My setup is:
Virb 1 - Virb Ultra 30 with ext mic for light aircraft intercom
Virb 2 - Virb XE with internal mix turned on
Same issue as yours: When editing the videos of each camera individually all is fine. Virb1 has intercom audio recorded and Virb2 has, well, engine noise. The issue starts in multicam mode, where no matter what audio source or what angle I select, the audio is always that of Virb 2.
Can't believe it's been 2 years and still no solve for this. Also seems that Virb edit hasn't been updated since December 2018. Not cool. I wanted to like the Virb Platform and G-Metrics + Virb Edit seemed a nice differentiator but now I get the impression that Garmin has neglected that line of business.
Make that 4 years. Still not working sometimes!