I haven't seen this before and wonder if anyone else has.
We shot a 40 minute clip on an AF100 and part way through the clip, the audio magically swapped channels. There's no mistaking it since the on-camera talent was wearing a lav and we ran the camera mic on channel 2. All of a sudden the camera mic is on channel 1 and the lav is on channel 2. Then after a few minutes it swaps back.
My guess is that in stringing together the 2GB files that make up the master clip, something went awry with one of the files and it and it alone has its audio channels misidentified. But I've never seen/heard of this before. We were able to fix it in post by slicing up that portion of the audio file and transplanting it but it scared the hell out of us (initially thought we'd lost part of the audio).
FWIW this is a Premiere CC edit with the media imported via the media browser. But I doubt it's a Premiere problem per se - we've imported tons of AVCHD footage before and never seen this. The footage had been copied to multiple drives and all copies do the same thing, so it has to be in the way it was encoded by the camera.