Aperture keeps multiple duplicate images in the library file which do not show up in the app

Question

So, I recently had to merge two libraries which have some common images.  Although upon import Aperture asked me if I wanted to "Add or Merge" the libraries (I selected "merge", which wouldn't import duplicates), I wanted to confirm there were no duplicates in fact brought in.  I ran Duplicate Annihilator, which made a strange claim (about most photos, in fact): it showed a file as a duplicate which had no copies that I could find - searching for it by name revealed exactly one image.
Curious, I searched inside the actual photo library.  Imagine my surprise when I found the following files
...Library/Masters/2007/Aug 10, 2007/IMG_0002/IMG_0002.JPG
...Library/Masters/2007/Aug 10, 2007/IMG_0002 (1)/IMG_0002.JPG
...Library/Masters/2007/Aug 10, 2007/IMG_0002/IMG_0002.JPG
which are in fact *exactly* the same image.  Meanwhile, to reiterate, Aperture shows only ONE photo:
IMG_0002.JPG
Shocked, I investigated further.  In fact almost every single file which was in common between both libraries was "imported but not displayed", which explains why my two libraries of sizes 50GB + 50GB after merger = 100GB when, the two libraries in terms of images had 10k + 12k after merger = 14k images.
Aperture imported all the photos into the new library.  But it just opted not to use half of them.
So, now I have a bloated-by-2x library, and of course the frustration with Aperture having made such an insane, bone-headed move.  Those files are essentially dead weight which will follow the library around for all eternity.
1) Why?
2) How to fix?
thanks!

Answer 1

I would take  a step back here before going further.  William's suggestion might very well clean up the library but something obviously did not go right and to start mucking about in the library might make things worst.
For starters I'm surprised to see the folder structure you showed in your first post. Aperture stores managed masters (originals) by import date and time. The structure (in all libraries I've ever seen) looks like:
So something seems wrong with your master folder.
Also the three folders you showed the first and third are identical ( the middle one has the (1) added to which is how the OS handles duplicates in a folder) so this shouldn't even be possible, those folders should not be there.
I'm wondering if this is something left over from your using Duplicate Annihlator. Do you have a copy of the library before you ran the merge and used DA on it? Would be interested to see what the master folder looks like.
Finally when you ran the merge which library did you tell Aperture to use as the master, the one that was used to resolve conflicts?
Again William's suggestion might be all you need to do but it would be good to figure out want went wrong before proceeding.
regards
Message was edited by: Frank Caggiano - A better first step might be to run the Aperture first aid tools, repairing and possibly rebuilding the library.