I recently offered suggestions for truly deleting Mail.app messages that routinely reappeared in Mail’s Trash. Reader Dave Birkin found no resolution in my advice and so followed up with this:
I have a nagging message sitting in my Drafts mailbox that stays there despite every form of deleting and “rebuilding” of the mailbox. Have you heard of such a strange behavior? I am running the latest version of Mail and tried all of your steps listed in your article.
I’ve not only heard of it, I’ve witnessed it. Try this:
Go to your user folder/Library/Mail.
Locate the folder that contains this draft—it might be called something like POPemail@example.com. Locate the Drafts.mbox folder inside this folder and then the Messages folder within that folder. Inside you should find a numbered file with a .emlx extension—something like 18391.emlx. That’s your nagging message. Toss it.
Launch Mail. There will likely still be something in the Drafts mailbox. Select it. You shouldn’t see any message body because you’ve killed the message. Now delete that entry, select that specific mailbox under Drafts, and choose Mailbox -> Rebuild. This should get rid of the message.