This is actually kind of embarrasing, but here it goes:
I've made a rough cut of some source material with 4 audio channels, channels 1-2 with environment audio and track 3-4 with interview audio.
Me being stupid, I did not enable the second audio track on the timeline onto which the clips where going, hence I've got a timeline with only the environment audio, but no voice.
Is there an automated way to replace the tracks? Edit done in cs6.
Best regards, Norway.
I found the solution my self.
Mark all the clips with wrong audio channels. Hit "Clip" on the upper menu bar, Modify>Audio Channels and do the replacement in the dialog that pops up.