Apple Mail Large Mailbox Error

If your Apple Mail mailbox gets too large, it may appear empty. You may also see the message "Message has not been downloaded from the server, take this account online to view".

This problem is not related to the number of messages that are stored on our servers, but rather to the size of the Apple Mail mailbox file on your own disk.

Please see Apple's support page that describes the problem in more detail, as well as the solution.