Restore flags, message folders, sent messages in Mail.app

My dad's computer has been running slow for some time now, so when we made the decision to upgrade it to Mountain Lion over the weekend, he asked that I do a clean install of it.  We backed up ~/Library/Mail, and once we finished the installation we put it back in place.  His inboxes and folder structure are all in place, however his sent messages, flags, and anything that he filed away into folders has disappeared.
We do have a time machine backup that was completed immediately before the install, and it's been re-associated with his machine, so in theory the information is accessible; I just need to know what to grab to restore it.
Thanks!

But are the sent messages also stored on the computer
Yes. The copies on your computer will be synched to match the copies on the server. If you disconnect your Mac from the Internet, you will still be able to view the mail prior to the disconnection. It's one of the main advantages that IMAP has over POP.
Note that there are behavior options for the Sent mail folder that change the retention levels:

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