Issue
A large number of users may be shown as Ownerless/Unassigned in the Bulk Mapping screen of Archive Shuttle:
BulkMappingPage
This could be caused by the fact that there are more mailboxes in the Enterprise Vault Directory database in the ExchangeMailboxEntry table for one EV archive, for example:

Firstly, start the synchronization of Active Directory, then from the EV Environment page in Archive Shuttle, Sync the EV Environment.
In the EV collector client logs you may see errors like this one:

2015-07-16 13:53:58Z|3966| 86|ERROR| ResolveOwner|Could not determine owner. Archive [user name] (15F59B235B83947448A4F70E43F7734301110000NOOSLKVS) has too many entries in ExchangeMailboxEntry table. Please correct this.

The following SQL queries can be run on the Archive Shuttle Directory database to check double entries

SELECT * FROM User where sAMAccountName like 'value'
SELECT * FROM User where UserSid = 'value'
SELECT * FROM ContainerToUser where UserSid = 'value'
SELECT * FROM ExchangeMailbox where OwnerUserSid = 'value'
SELECT * FROM EVArchive where ContainerId = 'value'

 
Solution

  1.  Delete the record(s) in EV database EnterpriseVaultDirectory Рdbo.Exchange Mailbox Entry, for Ownerless /Unassigned user
  2. Run Exchange Provisioning Task in EV console on EV source server
  3. Sync AD, Sync EV environment, and finally run Archive Gathering in Archive Shuttle

By following the steps outlined above Archive Shuttle will pick up the correctly provisioned archives, and they will no longer show as Ownerless/Unassigned.

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