Q: Lost Folders

Hi there, kathleenfromcanning,

I keep my emails in the Mail App separated with folders too, so I be glad to help get those emails sorted again.

OS X El Capitan: Recover items using Time Machine and Spotlight -- If you backed up your MacBook Air before updating, you can recover your email folders from there.

If some email messages or mailboxes are missing in Mail after upgrading to El Capitan -- If there isn't a Time Machine backup, use this article to help get those sorted again.

Mail (El Capitan): Rebuild mailboxes -- If neither of the previous articles have helped, rebuilding the mailbox may.

Hope this helps and thanks for using Apple Support Communities!