Directory synchronization creates linked Mailboxes in Exchange and does not revert them to regular mailboxes.
If the directory synchronization or migration sessions are configured to disable target accounts, target mailboxes will appear as linked mailboxes within Exchange.
Mailboxes are displayed as linked, because the associated account is set to the source user, and thus MSExchangeMasteraccountSID value is populated. This allows for proper mailbox access in certain situations.
See http://support.microsoft.com/kb/555410/en-us for additional information about this process.
There are two ways to change the mailboxes from linked mailboxes to normal mailboxes the following should be performed:
1) Migration Session
a. create a migration session within the Migration Manager project for all objects you wish to change
b. within the migraiton session settings, choose to disable source accounts and enable target accounts.
c. after the migration is complete you will notice that the source AD accounts are disabled, the target AD accounts are enabled, the linked mailboxes are displayed as user mailboxes. The associated external account will now be removed.
2) PowerShell cmdlet
Execute the following cmdlet in the Exchange Management Shell:
Set-User -Identity 'mailbox name' -LinkedMasterAccount $null
