Dear all,
This looks to me like a corruption of the Mail indexes, which I've come across a couple of times previously. I've found a solution that worked for me.
With Mail closed, in the Home | Library, go to Mail | V2 | MailData. Delete the three files with names starting with "Envelope":
- "Envelope Index"
- "Envelope Index-wal" and
- "Envelope Index-shm"
(Drag them to the desktop if you want to be cautious!) Open Mail again and it goes through an importing and indexing process, forcing a rebuild of the index from scratch, which resolved the problems that I experienced, which included faulty "read" count, missing folders, invisible messages, etc.
Good luck