Why are files going offline when exporting from premiere

Hi all
I've got a feature length documentary of 2 hours. All files are online but upon exporting from premiere via media encoder the finished file has 'media offline' on some shots. I have NO idea why this is happening. All clips are online on the timeline.
I'm exporting both blu-ray mpeg and dvd mpeg. The project is on an external hard drive. Can anyone help this is a nightmare!?
Will exporting via premiere pro direct fix this problem?
Thanks

Can't you see how the video is pixelated? Mainly around the nose and forehead?
Nope.  Looks fine when I watch it.

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    Can't you see how the video is pixelated? Mainly around the nose and forehead?
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