How can I force Apple Mail to COMPLETELY refresh an IMAP account?
I'm not sure if this will work for everyone, but I was able to resolve the issue in two parts. To get messages to display properly for all folders on the account, I needed disable/remove the account from iCloud so that it was no longer being synced. Then I removed the mailbox folder described in the question, and added it locally to the MacBook.

After the folders were displaying properly, the index was still a little messed up in that the inbox was displaying an unread count that didn't exist.

To get rid of this, I had to rebuild the full index -- this appears to be different from the Rebuild function that exists in the Mailbox menu, and is more similar to what happens when you open an upgraded version of mail for the first time.


Quit Mail
Navigate to ~/Library/Mail/V2/MailData
Delete any file that starts with "Envelope Index"
Start Mail
Follow prompts to allow Mail to rebuild the index -- this may take a few restarts of the app.