I found a way to clear the duplicates without clearing the whole akonadi 
database.

Close kmail and open akonadiconsole.
In the browser tab, right click on the collection/folder where you have 
duplicates.
Select the "Clear akonadi cache" context menu option.
Now open kmail and it will rescan that folder and hopefully the duplicates 
will be gone.

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https://bugs.launchpad.net/bugs/883459

Title:
  KMail duplicates emails

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