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