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They used Microsoft Exchange server which is a product intended for enterprise use with 10's of thousands of mailboxes (or more) depending on the version used. Exchange stores emails in a central database and applications like Outlook or a smartphone connect to that database to manipulate messages. If messages are deleted from the central store those messages will no longer be seen from the clients any longer. Once large chunks of messages are removed from the database Exchange "re-shuffles the deck" to shrink the database and they can be very difficult to recover.
Most phones and clients don't really hold a copy of the emails that can be preserved without the original data on the database. Clients can be configured to retain offline copies but in big businesses that is discouraged because the data becomes too hard to manage.
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