Invalid or Unsupported File

Hi guys

I have a big problem.
I am working on a project where I often have to go back to the on set recordings that the sound guy has provided me. They are recorded as Bwav 48khz 24bit files. Sometimes up to 6 embedded channels.
When I import these files into my project and i do any sort of process on them, or even just bouncing the clips, the files go missing the next time I open my project.
When I try to relink the media, Nuendo gives me Invalid or Unsupported file. When I go into my audio folder and try to open these files with any other program e.g. quicktime, media player, vlc, they are unusable.
Even opening them as Raw files in audacity just gives me digital rubbish.

I have done the following:

Copied project to new hard drive.
Back up the project out of Nuendo onto a different drive
Tried the same process on 4 different setups both PC and Mac on N 5,6,7 with the same results on all the systems.

Im working on Win 7 64bit pro, tons of ram, latest Nuendo 7 or 6.5 all drivers software firmware updated etc. etc. Fireface uc soundcards.

Any idea what could be causing this problem?
Its as if the header gets corrupted when Nuendo processes the files.

Any help would be greatly appreciated