Q: Apple mail accounts & boxes Missing

My problem was that two accounts did not appear in Mail (either in preferences or as mailboxes) but were showing in internet accounts and there were folders in ~/Library!

When I tried to add the accounts it said they already existed. Deleting from internet accounts then re-installing was the logical step, and it worked fine. A couple of days later and all still works as it should

I am glad that you got it sorted,  but, because they were showing up in internet accounts, they were probably already on your computer and just hidden.  You will notice a + and a hide or show button next to the mail boxes and hide was most likely selected.  Not to worry, as your solution worked just fine!   Tom

Thank you.

No, although they were on my computer  (I could find them in ~/Library but any changes I made to V2 and V3 folders had no effect at all) I could find no way of showing them in Mail. The + and - symbols did not work as when I tried to add it told me I already had the accounts, I couldn't delete as the accounts did not exist (apparently). Most frustrating, just glad all mail was on Google servers and easily accessible. In case anyone else gets this problem from the upgrade; however, there seems to be a wide range of issues from missing mail to completely unavailable mailboxes.

This is scandalous, really.  Apple must have known from problems in the beta that this difficulty could arise.    If they had said there is a possibility this will completely mess up your mail, I would never have upgraded from the last version.  The nice to have improvements are trivial compared to the time wasted trying to get this fixed.    

So far none of these excellent suggestions have worked for me.

Hi, I had similar issue and mine was solved my Eviscerator (Tom).

We may all have different issues so I'll summarise mine:

My inbox, sent, junk and trash folders were available no issue.

My iCloud folders were not showing.

When i clicked on the + button next to iCloud it (of course) offered to create a new mailbox (don't want new mailbox, just my subfolders back)

Solution - As Tom advised, when i hovered my mouse on iCloud, it offered both + and 'Show' options. Clicking on 'Show' opened my subfolders again.

Refer pic below if it helps.

Txs Tom!

ps Others may have different issue so wish you all the best.

Cheers

Stephen

I had the same issue. Pity Apple developers can't get the basics right. I had several mail accounts set up - two Gmail and three Yahoo. All had been made inactive except my main account which had been deleted and many years of mail stored on my Mac had disappeared. Its all still there though in ~/Library/Mail/ and its subfolders. Try this:

1. In the Mail Application click on File -> Import Mailboxes...
2. Check the Apple Mail option in the Import data from: box that pops up.

You can't actually navigate to the ~/Library/ folder as it is hidden but if you select your visible User folder the import seems to be able to find your mail archive and start to import the files. They will appear under an import folder in Mail and the folders will look different but all the mail is there.

Phew!

Hope that helps.

THIS IS HOW I FIXED IT!.

I had lost:

• all my folders (and of course the access to thousands of messages stored in them)
• all my Rules (automatic handling of incoming messages)

and rebuilding the mailboxes did not work.

Solution:

1. Started from the rescue drive
2. Re-installed El Capitan (overwriting the existing one (!WITHOUT FORMATTING THE DRIVE!)
3. Copied from time machine the complete "mail" folder  "user/library/mail" (overwriting the existing one)
4. Launched mail and it automatically imported the ALL the emails, including folders and rules.

Now EVERYTHING WORKS CORRECTLY.

I hope this will help you too.

I can see folders and mailboxes on my Mac, but they don't show up on my iPhone.  In Mail on my iPhone (iOS 9.1), when I switch accounts to Gmail, all my folders and mailboxes are there. When I switch to iCloud account, they are missing (except for default Inbox, Trash, Sent, etc.)

Please help.