Cloned system disc, all referenced Aperture files offline

Question

I was setting up my Aperture 3 library, all files currently located on the system disc as a trial of using Aperture, but I set up Aperture to use referenced location as I did not want all of the files (eventually well over 2TB of images) copied into the library. All was going well until my system drive started logging errors, the drive was failing. I quickly obtained a new drive, restored a recent backup to the new drive, moved it in as the new system disc and everything initially looked to be perfect. All applications launched, all of my mail, etc. was on the new restored system on the new physical system disc.
I opened Aperture, it launched perfectly fine, I selected a project, all of my thumbnails were there, so far so good. I then double clicked on a thumbnail to open the image for editing and no adjustments were active, the image was marked as offline, as were ALL images in the library for every project.
NOTE, NO files were moved, they are all still on the (new) system disc, as is the Aperture library.
I selected a project, selected one of the images in the library and then hit Command A to select ALL images in the project folder, go to the Locate Referenced FIles File option. Here is where things break badly. Nothing I have tried will actually let me select all images in the Locate Referenced Files dialog, if I try Command A I get the system warning beep and no files are selected. If I navigate to the first file in the selection of all images that I highlighted initially in the project folder to enable selecting the entire folder of images, I can select it in the bottom half of the dialog and the Reconnect and Reconnect All buttons activate but ONLY with the ONE selected image in the bottom of the dialog. If I hit Reconnect ALL ONLY the single selected image is reconnected. Nothing I have tried will actually reconnect all images.
There is no way I am manually going to hand select over 4000 images (in my initial testing of the library using images located on the system disc, but setup as referenced) by hand to reconnect them by hand. I am gun shy now about trying to use Referenced Files with my very large set of images, no way am I adding my over 2TB of images into Aperture using referenced files if I cannot guarantee if the images move, or apparently if the Aperture installation is moved to a new system disc, that I can still access all of the images without having to manually add each one by hand.
I have scoured the Internet looking for every hint I can to get the images back connected, but nothing has worked, other than manually adding the images one at a time.
Any ideas???

Answer 1

I would restart everything and try again.
In to top half of the dialog, select only one image. Do not try to select more than one.
Match it to the corresponding Master shown in the file browser in the bottom half of the dialog. Click "Reconnect All".
You might do this for only one Project. For me it's always worked regardless of how many Projects the files w. missing Masters come from. I filter Photos view for "File Status" is "Missing, select all, and bring up the Locate Referenced Files" dialog.
I have done this for hundreds of thousands of files with no problems. Aperture regularly loses some links to Masters, but I have always been able to reconnect every image.
If Aperture doesn't do it automatically, "Verify" your selected images by clicking the button on the dialog.
If it doesn't work on retry, then you would start to look into possible problems with naming drives and permissions.