IMAP was created primarily to support user's who access their email from multiple devices — even public computers. There is no rational way for that to happen other than keeping the files and folders (messages and mailboxes) on a central computer — ie. the IMAP server.
I have more than once had an email account get damaged on my computer and recovered everything completely by deleting the account from Mail and then adding it back. Once a connection was established with the IMAP server, voilá all the account folders and files immediately reappeared just as they had been before the damage occurred.
When you launch Mail the first thing it does for IMAP accounts is check in with the IMAP server and update the local "mirror" copy of the IMAP account contents on the server and it periodically synchs with the IMAP server so that each reflects changes that has occurred on the other. In ryck's case it is the local copy of the IMAP account's index that Mail is unable to "see". Whatever the glitch that is preventing its being seen it is fortunate that it has not been propagated to the clone.
