Message cleanup is performed separately from message archiving.
User Mailbox
Depending on what you configured in the Exchange user mailbox plan, you can:
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Stub, and then delete messages from the Exchange server.
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Delete messages from the Exchange server without stubbing the messages. This is also known as source pruning.
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Stub or delete only the messages that include attachments.
What Is Stubbed
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Mailboxes
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Disabled mailboxes
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Email messages
What Is Not Stubbed
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Non-email messages such as appointments, contacts, and so on
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Archive mailboxes
Journal Mailbox
If you enabled cleanup in the Exchange journal mailbox plan, you can delete the contents of the journal mailbox on the Exchange server.
ContentStore Mailbox
If you enabled cleanup in the Exchange journal mailbox plan, you can delete the messages from mailbox on the ContentStore Mail Server (SMTP).