I wish Apple paid a little bit more attention to their documentation. In the Apple Mail.app documentation, the terms archive and backup are used interchangeably. This could not be further from the truth. For years, IT guys have cried foul whenever this happens and have explained the difference in both methods. Just google the darn thing. If that’s not enough, take a good read at Robb Dunn’s post titled Personal Disaster Recovery: Backup, Don’t Archive!.
Contrary to the documentation, what Leopard’s Mail.app does when you use the “Archive Mailbox” feature is that it performs a backup, not archive. Your mail items are still available to you in the primary mailboxes.
