Q: mail folders disappeared on OS X El Capitan

I also have this same problem since upgrading to El Capitan on both my MacBook and my iMac. The mailboxes are still working properly on my iPhone and iPad with iOS 9.0.2 but are completely missing in Mac Mail.

Found the (an?) answer.

Go to Mail > Preferences > Accounts, and then uncheck the "Enable this account" option and then re-check it.

Worked for me

Worked the first time - Awesome...

Thank you! I was freaking out about my folders, and your suggestion worked! Easy!

Okay thanks! Inbox returned. Outbox still missing. Any thoughts how to get it back?

MrAll - The Outbox is only visible while it has mail in it, waiting to be sent. After the mail has gone (into the Sent box) the Outbox disappears.

My mistake, I had to translate it from my language. What I meant is that (old) data from my Sent box is missing (or not showing).

I have to say that, even though this fix is simple, it is anything but intuitive and not automatically importing folders is just bad design.

Mail account subfolders lost after update

And the fix doesn't deal with the fact that you can't move messages to the trash folder.  Any solutions for that?

I have just upgraded and find that ALL of my created mailboxes (ones that I keep in Mail and are only on my computer) are gone! I clicked on Rebuild but nothing has happened and now it's greyed out.

Will the Mailboxes I've created return? Where have they gone?

This doesn't work for me. I've tried this several times.

I've lost all of the Mailboxes that were 'On My Mac'. I've seen these referred to as subfolders.

I'm getting nervous now because I see that the uncheck, re-check fix is working for many people. Alas, not for me. I had about 20 sub mailboxes On My Mac.