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We are migrating users from Notes to Exchange 2010 using BinaryTree, some how we accidentally migrated users twice and it created duplicate items in the user mailbox.

Is there any powershell or vb script to check the user inbox for duplicate emails?

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No, there is not an easy way to achieve this. You usually don't access the inbox of users as this data is sensitive.

The most simple way I can think of is to delete the whole mailbox and reimport it. (But somehow I have the feeling you can't do that because the users are already using the new mail-environment)

Here is a technet aricle which describes how to remove duplicates in Outlook: How to remove duplicate imported items in Outlook

Anywho, you have to open up each inbox to find the duplicates. You could script this using powershell: Get-MailboxFolder

ForEach-Object $mailboxusers{
    $inbox = Get-MailboxFolder -Identity $_:\Inbox something with inbox here...

But for help with a script, I would ask on

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I know one could use this free app but its per user basis...

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