Render not happening right!

We might have done over 20+ client wedding videos in our Premiere Pro and rendered using Media Encoder.
Yesterday, we rendered one and after it got over, we found mid way, once audio was totally missing for 3 minutes.
Why would that happen ?
I thought, something went wrong with my premiere pro work, so I again opened the timeline and placed the audio and its was playing fine on premire pro preview same as before.
Then I again went to render and it pops up saying, some offline material in the render,bla bla bla.
I clicked on OKAY and proceed with render, as I know, all of my files are good.
In the render preview, now I see, the starting frames are all showing like red, not found.
But why is that ?

I think, I found the problem.
I updated to latest Premiere Pro CC this week.
And this problem has started after that.
All the sony NEX Camera files are showing as media file missing, while they are all exactly and correctly present too.
Those are .MXF and Sony AVCHD files.
How to debug ?

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