I see this is an ongoing thread. Frankly, there's nothing much any of us can do about Aperture losing its connection to referenced images. I've been using Aperture since v2. Its always had an issue in this respect. Fortunately, its simple to correct. Unfortunately, the next time you open Aperture, other images may be missing. The larger the library, the more problems.
Some thoughts:
Create a Smart Album with the source as the entire Library (Photos). Add File Status as a criteria and check the box. That will show you all the files that require reconnecting. You can actually select all of them, locate one of them, select reconnect all and Aperture will usually locate all the images, irrespective of whether they are in the same folder or not.
Every time you open Aperture, glance at the Smart Album. Its not unusual that there will be missing images (my Library contains 25,000+ images).
Note that Aperture can also assign the incorrect images to a Project. This also can happen over and over. What's weird is, on mine, Aperture picks up the same folder of incorrect images over and over. If this happens, delete the versions, don't trash the referenced files and reimport. This is bad as you will loose your edits. Unfortunately, you lost them anyway. Once you get incorrect images being referenced, you can't reconnect. There's discussion on the web that selecting the option key as you select reattach will do it. Occasionally it will, try it first, usually the reattach button will remain grey and you're out of luck. This has got to be as bug as I've had to deal with the same set of incorrect images being assigned to a variety of albums for well over a year. Has lived through even an OS X upgrade and the version upgrade to 3.4.5.
Repairing/ Rebuilding does nothing. The problem will persist. In ApertureExpert.com's post on reconnecting images, are the words "you may have to do this more than once". That's a polite way to say Aperture needs some work in this area.