On your Restore job, go into Microsoft Exchange, and then make sure the following option is ticked:
"When restoring individual mail messages and folders, restore over existing messages and folders.
Explanation from Symantec:
Check When restoring individual mail messages and folders, restore over existing messages and folders to replace an existing item with the message or folder. Check this when you are restoring from a continuous protection recovery point backup or from a backup that uses Granular Recovery Technology (GRT). A new object ID is not created for the message or folder; only the contents and properties are replaced.
If this check box is not checked, or if the original message or folder does not exist, then the message or folder is recreated as a new message or folder.
If this check box is not checked and if the original message or folder does exist, then the message or folder is skipped.
So if the email exists, it won't duplicate it. If it doesn't,m it will be created as a new message.
This is to e used when doing a GRT restore/backup.
Hope it helps?