How to move Mail messages from Apple Mail back on to Hotmail server?
Setup a second account in Mail for your Hotmail account. This time choose Exchange IMAP for the protocol, not POP3. (Use the server settings here: http://www.sirslur.com/2010/09/01/hotmail-has-imap-and-works-on-iphone/)
Drag your messages from your previous Hotmail account to your new IMAP-enabled Hotmail account.
Grab coffee and wait.


Sometimes messages will fail to sync. Just re-drag them as previously to re-sync them.