Oh, I get it, you want to remove duplicate >existing< files in your archive. I think any duplicate file finder will aid in that.
Maybe something here? duplicate text finder free download - SourceForge
Personally, I'd just move all the files currently in this directory into another one and zip it up into one huge file. Once company policy permits removing them, that file would go away. Zip compresses text quite a bit, esp. if there is a lot of duplicate text, which in this case there would be. Sometimes its just too much effort to try and do anything but the easiest approach.