How to rebuild mailboxes after "fixing" mail quits unexpectedly
How do I rebuild my smart mailboxes?
I lost all email after fixing Mail quitting unexpectedly
Aperture 3, Mac OS X (10.7.5)
Try rebuilding the mailbox.
Rebuild mailbox
If that doesn't work, try re-indexing the mailboxes. This can take awhile if you have a lot of mail.
Reindex messages For El Capitan, try looking in V3.
Reindex messages (2) See post by Linc Davis