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Sep 30, 2016 5:34 PM in response to fritzerby John Galt,Try rebuilding the Mailbox, or all affected Mailboxes, according to the following: Mail for Mac: Rebuild mailboxes.
It will take a few moments to complete, depending on the total number of messages in those Mailboxes. Until it finishes, it's normal to see the contents of Mail's message preview column flash or briefly disappear as it rebuilds the message database. Mail's operation will also be slow until it finishes.
It would be prudent to back up your Mac prior to doing that, but if rebuilding a Mailbox causes any email messages to be deleted they were probably not recoverable anyway. I recommend backing up in this particular circumstance only in an abundance of caution, but it's something everyone ought to be doing.