The first is to simply highlight the email and click on the REBUILD option. The mail will disappear. If this still does not happen, you can check out this post of onkeljonas from Ars Technica that shows you how to do it:
Poking around ~/Library/Mail/ showed that while Mail still showed the 1 unread message, it didn’t actually exist – it turns out that Mail needs a file to delete to be able to properly update the messagecounts and lists, and for some reason a mail file had disappeared by itself.
Here is a fix:
1) Navigate to ~/Library/Mail/
2) Open BackupTOC.plist, and figure out which of the entries under Root/messages is the borked one
3) Look at the kMDItemPath and make a note of the last part (xxx.emlx)
4) Open Mail, make a new draft, quit Mail
5) Navigate to ~/Library/Mail/[account]/Drafts.mbox/Messages/, make a copy of the draft you just created (don’t just rename it, or you’ll have to redo the process). Make sure the copy is in the correct mbox (in my case that was Drafts, so I didn’t have to move it) and name the copy using the note from step 3.
6) Open Mail, delete the offending email, profit!
The real problem here is how a mailfile went missing in the first place, but I’ll attribute it to some rare Mail bug involving empty messages.
Ho-hum. These are Leopard blues. I must admit, in terms of stability Leopard isn’t what Tiger used to be.