To help with this, you need to set up two more Smart Mailboxes.
Firstly set up a Smart Mailbox with these properties:
Note that I have included Sent messages so that I can track emails I have sent as well as those I have received.
This will give you a list of all the emails you have flagged. This is needed to help with the other Smart Mailbox which will list all the emails that you have yet to flag.
There isn’t a property you can set for a Smart Mailbox to make it list unflagged emails so you have to create one to list flagged emails and that the @Unflagged Smart Mailbox can check against. Sometimes you have to be devious to get Apple Mail under control!
Now you can work through your list of unflagged emails until they’re all flagged! Note that the @Unflagged Smart Mailbox doesn’t update itself whilst you’re in it – just click out of it (into the @Flagged Smart Mailbox for example) and back again.
During the day, when I check Mail, I just look at the @Not Flagged Smart Mailbox (instead of the Inbox) and process them with the appropriate flags. I then click on the @Flagged Smart Mailbox and back to the @Not Flagged Smart Mailbox which should now be empty (Mailbox Zero!).