If anyone would have bothered to try out some settings in Mail->Preferences->Viewing tab, then you might have noticed that there is a check box option towards the bottom of the window under "View conversations", and if you have that checkbox selected, it will show you such "duplicates". If you uncheck that box, all your problems will be resolved
Another solution is to disable Mail's detection of duplicate Message-ID's.
See this this excellent suggestion by Tom Francais:
In short, use the Terminal to change Mail's hidden setting after quitting Mail.app:
defaults write com.apple.mail AlwaysShowDuplicates -bool true
From then on Mail will happily show all messages with duplicate Message-ID's.
Kevin Strong wrote:
Of course, Apple should still really fix the bug they have of false detection of duplicates, but I don't to worry about that now.
False Detection? Kevin Strong is correct. Email duplicates are falsely detected, and this can lead to loss (not being able to find) important email.
Worse yet, if you want to prove in court that you sent something, it might not be enough to show a copy from your Sent folder, because the SENT copy does not contain the HEADER information that a received copy contains.
For that reason, I always Bcc a copy to myself, and keep the copy I recieve (not the copy in my Sent Folder.
When searching for an email (subject:evidence), I might only be shown the copy in my Inbox, leaving me to believe that I somehow deleted the copy with the important header information.
Thanks also, to Tom Francais for the solution for turning off this new "feature".