Mail obsessed with an old message
The mail database is probably messed up a little. You can often fix mailbox folder issues by rebuilding them. It's easy to do.

Open Mail.app and select the mailbox with the email in question. That's the MAILBOX not the message. From the Mailbox menu select "Rebuild" (at the bottom of the menu) and let Mail do its thing. Depending on the size of the mailbox this can take seconds or quite a bit longer. When it is done I usually quit mail and re-launch. Not sure of that is strictly necessary though.