Solution

Use these steps, one at a time, until the issue is resolved. Note: If you wish to back up your Mail messages before troubleshooting, make a copy of the Mail folder on a different disk (but leave the original Mail folder where it is). The Mail folder is in your Home folder's Library folder (~/Library/Mail).

1. Try rebuilding the Mail mailbox where messages are missing or can't be opened.

2. Reindex all messages:
1. Quit Mail.
2. In the Finder, choose Go To Folder from the Go menu, and go to ~/Library/Mail/ .
Or, choose Home from the Go menu, then open the Library folder, then open the Mail folder.
3. Move the Envelope Index file to a different location, such as your desktop.
4. Move any folders in ~/Library/Mail/ that begin with "Mac-", "Exchange-", or "IMAP-" to a different location, such as your desktop.
5. Open Mail. Mail will reindex all messages. This process may take several minutes depending on how many messages you have in your mailboxes.

I had to start a new account in OS X because my encrypted home dir would not mount. So I made a new account, mounted that image manually, and copied the mail and files over. But then the mail was not searchable.

Well, using this procedure it is. WOOT!