PhotoComix:
I think I remember that you are able to use a GNU/Linux OS. My first thought was that as long as the images you want to delete are clones with no difference in processing, then a nice little script comparing md5sum values should be able to find clones and then allow you to delete them. I did a search and found this site with two command-line scripts that you can run in a terminal window:
http://ajayfromiiit.wordpress.com/2009/10/16/one-liner-to-find-and-remove-duplicate-files-in-linux/What you will have to do is place one folder inside the other folder since the script gets run on the folder of your choice and all folders inside that folder to make the comparison. I tested the scripts on a small set of images where I made a copy of the original. It found the duplicates.
The second script on there allows you to search for the duplicates and will then ask your permission to delete all of the files before doing so.
I only use GNU/Linux so I do not know what may be available for users of Windows.