Help with duplicate delete

Short Description:
have 2 drives with 100's of duplicate files but completely different directory names and structures. How do I delete the duplicates?

Long Description: (skip to what I have tried if you want)
Scandisk automatically fixed a perfectly good 200 GB drive resulting in major corruption. I have recovered data and want to compare to my last backup. Recovered data will be 90% same as backup except that all the directory structure is blown away. If the file exists in backup I want to delete it from the recovered data leaving only changed files for me to have to sort.

What I have tried:
About 15 different compare applications. This one looks by far the most promising. Tried lots of things in beyond but this seems most on track.
Selected backup data in left and recovered data in right. Expanded all. selected all and compared contents. However it only found duplicates where dir structure was the same. What am I doing wrong please.

Hope I don't appear lazy as I am sure this will be answered elsewhere if I spent more time looking. I have spent weeks on recovery and comparison and I guess I am just a bit over it :-(

Thanks in advance
Mel

Well it appears BC cant do this??? Shame looked really promising. I would have thought it quite a common requirement but obviously not as all the file/directory compare programs I have tried fail in this respect. I have copied 2 URL's from elsewhere in the forum of applications that apparently can do this and I am off to try them. Will post progress for others who have similar issue.

Total commander (http://ghisler.com)

spaceman99 (http://www.extrabit.com/spaceman99/)

Well... not good news. Tried Spaceman, nice but no good for a side by side compare. Total Commander does "side by side" and it does "branch view" but damned if I can work out how to compare the duplicates yet alone delete them. I have tried another 10 products... no joy... will let you know if I find one.