Aperture is now in its 3.4.3 version. I've been having problems with several images disappearing just like that. One day my library is complete, the next day some images are missing (offline).
Curiously, I've always had a managed library from an external drive, and none image is referenced, in order to avoid such offline issues. I created a smart folder with the only condition as "label is offline", in an attempt to track missing images. Well, no matter if I rebuild or repair the database, several images still show as "offline" on a daily basis. Then I check the Aperture package, and yes, I confirm that those images are nowhere to be found in its folder/project. Sometimes I take notice after syncing my iPhone with iTunes, and I got a message "x images were not copied because they couldn't be found".
Luckily, I always have several backups, so I just reimport the missing(s) image(s). But why should I do that? Sometimes they are so many (30, in one case, from different projects). Most of them, by the way, are images copied from my Photo Stream, but not always.
I've exchanged emails with an Apple Support guy in recent days. They actually don't have an answer to this annoying bug. I've started to lost confidence in the safety of my photos in Aperture.