Premiere Overwriting Media Files

Having a serious problem. Editing a sequence with video footage from a Canon 5D and 7D, and an audio track in WAV format from a Xoom recorder. Attempting to cut the audio to replace camera audio.
After working with the project for a couple of days, Premiere appears to have overwritten a number of the ORIGINAL audio files on the hard disk. The affected clips in the timeline appear with bold hashmarks through them (the track is not locked, it is only a random selection of clips in the timeline that are effected). When the sequence plays, there is no audio from these clips. They no longer display a waveform in the source monitor.
Further, the link to the orginal media is no longer present (the opotion to "reveal in finder" or "reveal in Bridge" in the project panel is greyed-out.
When I search in the media file folders on the har disk, I find that the original files have been changed at the time the clips became inaccesible. When I attempt to play them in Quicktime or Quickview them, they open showing no contents (0.00 start time and 0.00 duration), though the files still display a file size (i.e. 7mb).
We have replicated this problem storing our project (and its corresponding media folders) both on a shared raid drive on a workstation and on a striped raid drive on a shared server directory.
Hardware/software info as follows:
Editing performed on an iMac i7 2.93 ghz, 8 GB ram, ATI Radeon HD 5750/1GB, Premiere Pro CS 5.03
Files located on a Mac Pro Server 3.2 ghz Quadcore, 8 GB ram running OS X Server 10.6.7 with a 2 TB Raid 1 (2 x 1 TB Drives Striped).
Previously the files were on a Mac Pro Workstation, OS X 10.6.7 with a shared 4 TB Raid 1 (2 x 2 TB Drives Striped)
Any help would be GREATLY appreciated!
Thanks,
David Breen
Creative Director
Canadian Forces School of Aerospace Studies
Department of National Defence
Government of Canada

Premiere may be non-destructive, but I have had it break files before, in a manner similar to what you're describing. In my experience, this has been tied to the "Write XMP ID to Files on Import" option in Edit > Preferences > Media.
With that option enabled, Premiere will write some metadata into an imported file which it then uses to keep track of the file as it travels through the Adobe applications. I've had a few instances--both with specific file formats (SWF is an example) and with random individual files--where that process effectively broke files both in Premiere and on the desktop. I've actually rescued a few files by opening them up in a text editor, deleting the metadata (it's visible as XML), and resaving the file--it imports and plays properly, then. Of course, if you don't disable the "Write XMP ID" option, it happens all over again.
Not saying this is specifically what is happening here, but here's a test if you're feeling enterprising:
Find a file (WAV, for example) that hasn't been imported into Premiere yet. Make a copy of it with Explorer.
Import one of the copies into Premiere, making sure the "Write XMP ID" option is checked before you do so.
Grab and install WinMerge, which is a great little program for comparing two files. It will have an option to add an Explorer context menu item to "Compare" files--this makes it easy to do just that.
Using WinMerge, compare the imported and the not-yet-imported WAVs; near the top of the file that was imported, you should see a few lines of XML data, while the file that wasn't imported won't have this. WinMerge keeps the scrolling synced so you can easily see differences between the two files. The rest of the file will be all binary mish-mash, but you should be able to see where the metadata is inserted--make a note of that.
With Premiere close, find one of your "damaged" WAVs (make a copy of it, just to be safe), and open it up in a text editor; I'm partial to Notepad++. Pretty quickly, you'll be able to see the injected XML metadata. Simply select it and delete, making sure to delete only the parts that weren't in the non-imported file above. It should be pretty clear where that is, but just in case, that's why we made a duplicate first.
Once you delete the metadata, simply save the file, and try playing it back in whatever player didn't work correctly before. If it works (here's hoping!), give it a shot in Premiere. If it works there, I'd suggest fixing all your broken WAVs, and then opening them in an audio editor of one sort another and saving to new files (same format). This will basically just repackage the contents of the file in a new container that hopefully won't break again if you re-enable the "Write XMP ID" option (which is a good idea).
If that doesn't work... well... we'll cross that bridge later

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