Files Suddenly Missing with strange size behaviour

This morning I was looking at one of my work folder and noticed some subfolders were missing, upon looking further in the subfolders: basically everything was missing — except files that were locked. I checked the root folder where all the missing folders used to be and the file size was 31GB, which was about the correct size if everything was in there.
I did a 'ls -a' in terminal and only the locked files were listed.
I did a Permissions verification and Disk verification and it reported no problems.
When I restarted my computer hoping it was just a weird bug, the folder was still the same with only the locked files there, doing a Show Info to check the file size this time returned 30MB which was just the locked files.
I've done research but haven't found much useful about why this would have happened and how to recover it! I'm quit anxious about this since the last backup I made was about 4 weeks ago.
The only thing that has been different was that this week I used another MBP to access my computer via Shared files, but I logged in as the admin so that I could read and write files remotely. I did not do anything other than copy and write some files (I don't think I did anything in the folder with missing files) from the other laptop. I can't imagine how this would cause so many files to be deleted.
What's the best way to recover such files? I know the extension of the missing files — most are the same few kinds of file.
Is there a log somewhere that might reveal what program/process deleted the files?
Is there a log to see what files have been deleted?
I appreciate anyone reading this and any help in advance.

Ok I have deleted and rebuilt thumbnails files to no avail.
What appears to be happening is that aperture is using the wrong file-path for the affected pictures.
I keep all pictures arranged by date order so for example where the correct file path for an image would be;
Raid Zero/Pictures/2006/0609/060928/pict3722
Aperture is giving a file path of
Picture Library/2007/0712/071223/_DCS1023
in the manage referenced files pane it shows the wrong path as above, the thumbnail picture is of the wrong file but the thumbnail name and date is correct.
Interestingly since rebuilding the thumbs it is now possible to reconnect to the correct original file whereas before the reconnect option was not available, however it is only possible to do this one file at a time,the re-connect all function does not work presumably because Aperture is not aware that its filepath is wrong.
Oh dear.... Aperture has just crashed,this immediately after reconnecting 6 files and waiting for the files to update to the correct image in viewer mode.
GRRRRRRRRR!

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