missing mail

I had the same problem. To be clear, the folders that were missing for me were Personal folders and all were for POP accounts.

I solved it by first creating a new personal Mailbox with a distinctive name "On My Mac".

With Mail quit, next I went into the ~/Library/Mail/V4 folder and looked into the folders that had various alphanumeric names until I found the new one with the distinctive name.

I then opened up my Time Machine disc from the Finder and drilled down to the last backup from El Capitan and went to the ~/Library/Mail/V3 folder and found my previously saved personal mailboxes, and dragged the smallest one to the folder in the V4 hierarchy with the newly created mailbox in it. I just used one mailbox to test whether the process worked.

Once it had copied across I went to the ~/Library/Mail/V4/Maildata folder and deleted any file with "Envelope" in it's name.

I then restarted Mail, and got a dialog that it was importing mail and once it completed, my personal mailbox had been re-created in the macOS Sierra Mail app.

Next I repeated the above steps with all the other remaining mailboxes from my old V3 mail and once they had all copied across, deleted the "Envelope" files again. This took quite a long time as there were quite a few years worth of mail to move over but it has worked perfectly since then (as far as I can tell).

Hope that helps.

If it is showing in your list of folders in the Mail app, it must be somewhere. Maybe drag some messages into the new mailbox first and then look again - I think I may have done this. I'm not sure if deleting the envelope files at this stage will help to show it up but it might be worth a try.

Glad it worked.