I’m all of a sudden experiencing a similar problem on a much simpler level. I recorded a play using a shotgun mic for house ambience on ch 1 with a line feed from the audio board on ch 2. Upon importing, FCPX 10.4 only shows ch 1 (on 4 channels!). And even though I had the line feed going into channels 3&4, the audio from ch 1 appears there as well.
I’ve never had this problem in the many years I’ve been doing this exact same thing.