Premiere Pro CC (2014) has ERASED AUDIO from my original media?

Question

I know there are a lot of threads out there about not hearing audio, or missing audio. Maybe this is a related problem, but I didn't find anyone who described the same problem I'm having, or had a solution.
I opened up a project today that I've been working on for a few months, a documentary of sorts, with interviews, b-roll etc.  I'm editing with the native footage, which is AVCHD, shot on a Panasonic AF-100. Today, I noticed that two of my interview clips seemed to not playback as I watched it.  I wasn't too concerned at first because I know PP can be buggy, but here's all the things I did and how the problem escalated:
- I tried playing it again, to see if it was a fluke... no audio
- I looked at the audio in the timeline... no waveform, just a flatline... no audio.
- I looked at the whole interview's audio waveform... about HALF of it is FLATLINED... like PP had erased or overwritten the audio somehow!
- I restarted PP... no audio. Then I restarted the whole system... no audio.
- I went back to the original clip in the Media Browser to try to re-import it... no audio.
- I opened Prelude to try to look at the original media from different software... no audio.
After a few months of work (and an editing budget of tens of thousands of dollars), I am 4 days away from the delivery date, and PREMIERE IS ERASING MY MEDIA!!!
If this is not solved, I stand to lose more than just this job, but this entire client, my reputation, and my livelihood. ARE YOU LISTENING, ADOBE?  This is my career we're talking about. Please help.

Answer 1

Thanks for the reply shooternz, to answer your questions...
Any recent updates? eg O.S
- Nope. I'm running OSX 10.9.5 on a 2014 Mac Pro.  I've been told to avoid Yosemite at all costs.
Have you checked the source files of the affected clips in another player?
- Other than Prelude, no. One thing I hadn't tried yet was to fire up my old version of Final Cut and see if I could transcode it from there with audio.  What other player can read a raw .mts file?
What does the Clip in the Bin and the Source monitor indicate ( Info)
- The icon indicates that there's audio, and when I look at the waveform in the source monitor, it looks like just what I hear... a few minutes of regular audio, then flatline, then some audio again, then flatline.
Have you tried your back up project file?
- No, I didn't want to lose the editing progress I had made today.
Is the audio from camera or from other recorders?
- from the camera
Anything common between the affected clips? eg merge, FX,
- not that I can tell, at least nothing that wouldn't also be true of a dozen other clips which seemed unaffected. no clip effects, etc.
What does the Audio Mixer and Audi Meter  show?
- shows nothing (where it is flatlined in the original clip) as I would expect.
AFAIK - There is no way PPRO can "erase" just the audio from your source file. At least not without the editors input.
- That's what I would think too. But even if it's not "technically" possible, it seems to be "effectively" possible because nothing in the creative cloud seemed to be able to read the clip properly. As I mentioned in my post above, it seems to have only been solved by relinking the clip to a .mts file recovered from a back-up of the project from a couple weeks ago.  Though, for what it's worth, the file sizes are identical and created/modified dates match as well... so yes, it would appear that the file has not been altered, but regardless, I can't point to it and get the proper audio.