Bookmarks are gone
Since the last Security-Update 12.05.2006 all Bookmarks in Safari are gone. After the restart Safari started blank and all Bookmarks were deleted or ??. Is there any chance to find them again somewhere? Bookmarks.plist. is empty.
Surprised to hear the Security Update affected your bookmarks file. I haven't seen this reported by anyone else.
Did you do a spotlight search for Bookmarks.plist? Do you see a copy other than the one in your Safari folder? If that file does not exist, you will need to recreate your bookmarks, certainly not a pleasant task.
I back up my system to an external drive, so there is always another copy of the Bookmarks file on hand. Also, once a month, I make a copy of the Bookmarks file on my HD. This is a "just in case" copy - just in case I need the file and the external doesn't cooperate.