For a one-off issue, manual is going to be easiest by far I'm afraid. Unfortunately, most Notes installations do not include much in the way of automation help.
Development for Notes is a rather specialist subject so resources and skills are few and far between.
To do it manually:
Change the sorting on the view containing the mails so that they all appear together - probably by sorting on "Subject" or maybe "Who". Then, holding down the shift key, use the arrow keys to select all of the duplicate mails. You can then delete them.
I note that in Notes 6.5 the default Inbox doesn't allow sorting on Subject for some reason.
You could also create your own View - I have two additional views that I always create - "All By Date" and "All By Person" which include ALL mails (sent as well as received, calendar & email). Unfortunately, I can't give you a simple formula here to create a view due to the nature of the View designer in Notes but it isn't too hard - you may need to look up the help though as your admins may not have included the development help files.