Q: 10.11.2 El Capitan: Mail keeps quit and asks for rebuild

Me too. Just installed ElCapitan and Mail is just impossible. preview pane is there, but no body in messages. 'Downloading 13 of 46 messages' or some such is always in the activity window. Changes with each time I reopen Mail. then on reopening, I have duplicates of msgs that I deleted previously.

It has something to do with icloud, but I don't know how to fix it.

this discussion from October might be relevant…I will try to work thru it.

Re: Mail:El Capitan: Emails not shown

Same problem here, but only after updating to 10.11.2. I also noticed that this version added a 'Deleted Messages' folder under iCloud that I did not have before. Here's what now happens …

1. Delete mail (inbox, sent, draft), empty trash, but emptied trash immediately reappears so I empty it again.

2. Quit Mail.

3. Re-open Mail and all of my deleted email is re-downloaded and reappears.

4. Then 'Downloading Messages' stops at a number (different each time) and doesn't complete so that new emails have no message in the body of the email.

Hope Apple fixes this soon … Mail is very difficult to use at the moment.

this may have done the trick: http://www.scrubly.com/blog/how-to-mac-mail/how-to-fix-common-issues-in-apple-ma il-by-rebuilding-and-reindexing-the-mailbox/

It is for older version, but seems to be making more sense now. Still downloading msgs.

I deleted a couple thousand emails before doing the manual rebuild

PS: in these instructions, the new folder is V3, not V2, but seems to be doing something.

Thanks gretta. Tried the manual reindex outlined in http://www.scrubly.com/blog/how-to-mac-mail/how-to-fix-common-issues-in-apple-ma il-by-rebuilding-and-reindexing-the-mailbox/. 'Downloading Messages' no longer stalls, but otherwise I still have the same problem …

1. Delete mail, empty trash twice (emptied trash immediately reappears so I empty it again).
2. Quit Mail.
3. Re-open Mail and all of my deleted email is re-downloaded and reappears.

Yep, no solution here either. I have blank messages, but only some/most of them. And the 'downloading' never changes and nothing is ever downloaded.

Mail in icloud and iPad work fine. I hope someone is working on this. It is a sync issue, is it not?

  another good thread     

I did as suggested there:

- deactivating all accounts; (Mail>Accounts, uncheck the box Mail under each account)

- quitting the app;

- deleting the Mail folder in the Library folder of my home; (hold down option to select Library in the Finder>Go menu)

- rebooting the computer with reset of the memory controller;

- on another computer that does not have the same issue, deleting …a lot of old emails

- restarting Mail

- reactivating my mail accounts

and seem to have success this morning (but as with Pascal, I'll have to wait a while to be sure.

But as of now, the emails all downloaded instantly, none are blank, all syncing correct/matching emails I read or trashed last night on iPad, CPU usage is at 4%, Not sure about 'memory controller', but this doesn't seem to indicate that Mail would be affected.)

Also, to be safe, rename your Mail folder in the Library instead of trashing it. Then when the new Mail folder is rebuilt correctly, you can trash the renamed one.

Best of luck and happy holidays to all of us.

Let me jump on board too. Mail is just downright buggy. As you create a new message, it stores "saves" in the Drafts folder. I recently sent out a short e-mail to friends, and it must have saved about 30 "saves" in my Drafts folder. So I delete them one by one, but when I would Quit Mail and then immediately go back in, EVEN MORE versions appear!! The short term solution is to go directly to iCloud and delete all of the drafts created, and then they don't download to your Mac. But, of course something is wrong with Mail after this last El Capitan update. It is frustrating and barely useable due to that frustrating feeling! CONSTANTLY DOWNLOADING MESSAGES!!

I'm experiencing the same with auto saved drafts, however in my case they return even after I have deleted them in iCloud – first reappearing in Apple Mail and then also in iCloud Mail. They simple cannot be deleted, and they seems to replicate so that I get 5, 10, 20 of the various stages of each auto saved draft that comes back over and over again … very frustrating!

I'm also still experiencing stalled downloading of email. The header and subject show up but no message in the body of the email. The bottom left just says downloading 'x' of 'xx', but doesn't complete this operation. I have to quit Apple Mail, open iCloud Mail, open every email (read), then logout, open Apple Mail after which they will download.

These are very serious issues that only started happening with El Capitan 10.11.2. I've never had any problems with Mail prior to this update.

I hope Apple fixes this soon!