The work around for Duplicate Emails is as below: - ( This is a Per User workaround)
NOTE: - BEFORE PERFORMING THESE STEPS, PLEASE CONFIRM THAT THERE ARE DUPLICATES TO ALL THE SHORTCUTS ELSE DO NOT PERFORM THESE STEPS.
1. Open Outlook
2. Open Advanced Find (CTRL+SHIFT+F)
3. Click on Advanced Tab
4. Change the FIELD to MESSAGE CLASS | CONDITION to 'contains' | and type the VALUE as IPM.NOTE.ENTERPRISEVAULT.SHORTCUT
5. Click Add List button and click Find Now...
You will find all the EV mail shortcuts and you can select all and delete them.
The underlying problem here is that Enterprise Vault no longer makes shortcuts out of calendar items when archiving them. The most it can do is strip attachments from the calendar item and replace that with a link within the calendar item itself.
So when the calendar items were restored, there were no shortcuts to replace. That being the case, the workaround where you'd be looking for the shortcut message class wouldn't work either.
The issue at this point is that of having duplicates in Exchange that have no real relation to anything Enterprise Vault-specific. So unless Microsoft has some sort of tool that finds and removes duplicates, there's no viable solution.