Suddenly renames  files edited with external editor

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Not sure what I have done but now when I "edit file with..." (Photoshop CS5) using Aperture3 the version name is changed in Aperture.  Looking in PShop it is dislapying the correct masterfile name but on return to Aperture3 it is changing the version name. When I have finished in PShop I just close and it says "save". I click "Yes" I don't do any "Save As..." to confuse things.  Aperture is now changing the version name using a prefix and counter that I used for file imports on a job about 3 shoots previously so not even the most recent one!  How do I get it back to creating a version (PSD file) with the same name as the master.
Thanks for reading this.
Jules
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Replay

Thanks TD for your input. While I could not get the rebuild to work (it would show 97% done then hang up), it helped me isolate the problem. I ended up deleting all the images that were edited by PS CS4 then tried to do the rebuild again. Still no luck. I then opened the file sans the edited PS images and it worked.
I then edited one of the images using PS CS4 as the external editor and that worked. I then exported the image to the desktop and that also worked. The only think I can think of is that the original edits were done in iPhoto 9.0 and I have since updated it to 9.1. Whatever - it works and the only loss were some edits on a dozen or so family candid shots.
Your help in getting me headed is most appreciated.
Ed