I have found a fantastic script by Jarno Elonen to delete duplicate files on Linux.  This is very, very helpful to delete duplicate emails in Maildir format, apart from other normal files.

Here is the link to the site:

http://elonen.iki.fi/code/misc-notes/remove-duplicate-files/

In case the website is not accessible, leave me a comment and I will send you the script.

Enjoy!