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e.g. if you delete a picture in aperture 3, it won't delete the original photo on the hard drive.
That is designed behavior. Aperture is all about protecting your master file for each shot (wherever it is stored). When you make edits, it doesn't actually change the master file either. And when you delete (or move a shot to Aperture's trash) you are only removing it from the Aperture library. The master file, as always, remains untouched.