OS X Mail not showing Archive mailbox (and lost Flagged mailbox)

Recently I notice the Archive mailbox in Apple Mail has dissappeared. I can find messages in that mailbox using Searchlight if I know the exact contents of the message or subject but I use this mailbox to store application licenses, etc., and do not always know the right subject. I used to browse, knowing roughly the time when I bought the licese. Also the Flagged mailbox is grayed out in the favorites line and not shown in the left hand mailbox side bar.Also a pain because I set reminder messages and conference call emails with colored flags.
Any help?

Next to the On My Mac there is a hide function. Did you select it? If you go to the same place, see if there is a Show function.

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