Cannot reconnect images that aren't referenced

I have been using Aperture 3 and Lightroom 3 together to edit my images. Unfortunately LR3 has reorganised some of my Aperture 3 images into a folder not assigned by A3 inside of the Aperture library, now A3 cannot find the originals and asks to reconnect them. When I try and reconnect it says 'The selected master image is either offline or not found. Please reconnect it and try again.' Why can't A3 be told where the masters are, instead of refusing to find anything that's not referenced?
You can even do this in iPhoto, do I have to re-import the originals?

You can't 'reconnect' managed masters. Aperture expects them to be in the library where it put them. They have to be put back in exactly the same place and with the same name. Which is why going into the library and messing around is a really bad idea. The best thing thing would be to restore from your backup.
You need to rethink your setup of using both LR and Aperture this will happen again.
Message was edited by: Frank Caggiano

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