I'm having the same problem ("The original file and new file have different audio source and channel counts"). after moving my original media from one drive to another. But the destination drive (WD 3TB My Book) was properly formatted in Mac OS Journaled format. I've tried trashing fcpx 10.0.6 preferences with no luck.
Footage from a gopro and audio files are relinking Ok, but all the videos from a Canon 5D are giving me this error.
Any help appreciated,
I may have missed it but what format/codec are your original files?
Long shot, however worth a try, take one of the files put it through compressor and back out the otherside as the original file type.
I had a similar issue and had to do a manual replacement of the clips, the timeline does give you the original in and out points of the media which does help the process along.