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It sounds like you've configured Outlook on your desktop computer to connect to Exchange via the POP protocol. I'd recommend changing this to MAPI. However, if you need to use POP, there is a section in the account settings you need to tweak to "leave a copy of the messages on the server." Having this setting unchecked will result in the messages being downloaded. Hence, when you connect to your desktop Outlook client your mailbox is empty.
There isn't an easy way to copy the messages back. You could take another Outlook profile, create an IMAP profile connecting to the same mailbox and use a .pst file to drag and drop all of the messages back into the mailbox. Alternatively, you could just email messages of interest back to yourself.
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