I "solved" the phantom count on my Mail app Unread smart mailbox by adding a criterion for the account and narrowing it down a little used email account of mine.
When I logged into webmail, I discovered an unread message that Mail app somehow didn't download, but still registers as unread. When I marked it as read in webmail, the unread count disappearing in Mail app.
But now I see that the server messages counts and Mail app message counts differ for a lot of mailboxes! WTF?
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