I’m having the exact same issue too, years later…
I’m using the same project file in two locations, one in my bay where the media is on a SAN, then I will move the file to my laptop and use the same copied media on an external drive.
The audio files recorded with a Marantz flash recorder are off–usually seems to be 45 seconds(!) whereas the audio files recorded with a different recorder (maybe a Sound Devices?) reconnect fine. The video is from a 5D.
This baffles all of us in the department.
Seems to be a very rare problem, but if anyone has any ideas please comment!