Did you see thisthat has a possible answer for you?
just to be sure - you looked in the System Library directly on your MacintoshHD and not in the Library in your Home folder? And the ProApp System ID is missing?
Sometimes Aperture writes this file to a temporary directory, when it cannot write to the Library. If the above does not work, look at the temporary directory /tmp
- Use the Finder's "Go" menu
Go > Got to folder and enter /tmp into the textfield. If you see the file there, move it to its proper location in /Library/Application Support/ProApps