lose of mailboxes since downloading El Capitan OS

Please select the Accounts tab in the Mail preferences window. Do you see all the mail accounts that you had before the upgrade?

And do you have the messages back?

I clicked on "enable this account" under IMAP and all the messages returned!

I was storing them on my iMac in smart / mailboxes

You were not storing anything in smart mailboxes. A smart mailbox is merely a saved Spotlight search and doesn't contain anything. Do you mean "On My Mac" mailboxes? What backups do you have? What kind of mail accounts are these—IMAP, POP, Exchange?

THANK YOU SINGING TRAVELER 🙂🙂 - after upgrading El Capitan I too lost my 'OnMyMac' mail boxes which had actually synced to iCloud so they were about!

I have followed up sooooo many suggestions over the past week without success - many hours of investigation!

Your action - 'I clicked on "enable this account" under IMAP and all the messages returned!' worked!!

Simply, I traversed Mail Preferences, Accounts and while the ENABLE THIS ACCOUNT BOX was ticked, I UNTICKED IT and RETICKED IT ( FYI, the one account was actually an iCloud IMAP ) - 37 personal mail boxes reappeared in my Mac Mail - BRILLIANT 😍 and so pleased!