Use Referenced Masters To Avoid Accidentally Deleting A Master Image File

Question

If you use Managed images it is possible to delete the master file accidentally.  If you delete versions of an image using File -> Delete Version and the version you are deleting is the last remaining version for that image, Aperture 3 will delete both the version and the master image.  If you subsequently empty Aperture Trash and then System Trash that master image file is gone forever.  In Aperture 3 there is no warning that you are about to delete a master image. 
A workaround (although a weak workaround) is to use Referenced Image Masters.  Then when you delete the last version which includes the master image from Aperture, you can uncheck the box "Move referenced file to system trash." and no master image file will be deleted.  The downside to this workaround is that when you really want to delete a master image file, it must be done via Finder.
The best solution would be for Apple to fix this bug so that when you select "Delete Version" it only deletes the version image and reverts to the master image.  That way the master image can only be delete via the command "Delete Master Image and All Versions."

Answer 1

There is no bug there.
I had some trouble wrapping my mind around the file-Master-Version-Image-(Preview) complex that flows, sand-like, through the entire working of Aperture.  (I like a thing to be represented by itself and itself alone, and to exist in one place and one place alone.  I was comfortable with the seeming precision of the location-based "file+path" metaphor for the existence of these virtual things.  Aperture quite cleverly moves beyond that.)  Two things helped me move forward:
- understanding the difference between Projects and Albums, and
- separating my Library into a storage area and an output area.
Projects are, for me, storage containers.  (I have said elsewhere that the mis-naming of "Projects" is the single worst interface decision made in Aperture.)  They have a privileged relationship with your Images:  every Image must "live" in a Project, and "lives" in only one Project.  It may help you to think of "Image+Project{Path}" as functionaly equivalent, within the Aperture Library, to the file directory "file+path" mentioned above.
Albums are, for me, output containers.  I create Albums every time I know I will output a set of Images.
In practice, I work on Images in each.  In general, I develop my digital captures in the Project that holds them (and I rigorously stick to "One Project = One shoot"), I create Versions and add them to Albums as needed for output (they are automatically made the Album Pick), and I tweak them for output and then output them from Albums.
You may be wondering (if you've read this far) -- "What has this got to do with deleting Masters?"  A lot.  Note the difference in the context-menu between a Version in a Project and a Version in an Album.  The menu for the Album contains two delete commands: "Delete Version", and "Remove from Album".  The Versions live in Projects, and only visit Albums.  As Terence correctly points out, if you delete the last Version, your expectation should be that you are deleting that Image from your Library.  My suggestion is that you adopt something similar to what I've set up, and delete Versions from ONLY Projects (never from Albums).  This way you will never unknowingly delete the last Version (because Images can be in only one Project, and if you delete the last Version from that Project you know you are expunging that Image from your Library).