Q: El Capitan dowloaded now have lost emails

IT should be in your library.  I was able to get all my mails back by following exactly what Eric Root said about re- indexing.  Is your library hidden? 

I had similar issues even trying to rebuild the mail box.

ok i found those folder and deleted.. its recovered some but not all the emails.. a royal pain in the A. Thanks apple

Any other annoying things likely to happen with this latest upgrade?

Have you tried sending mail? I had a problem with that at first too but all i did was re type my password in the smtp account and it worked.

Crap update . Yes Apple, it takes Mac experience to New heights (finding lost emails!)

Hi, I think to have solved in this way:

first of all I made a backup with Time Machine before install El Capitan

I have downloading El Capitan and create an installation point by a USB memory (at least 8 Gb) using DiskMaker

I have installed El Capitan as new machine

Data restored from Time Machine after reboot

All POP3 emails are charged again

yes I have a problem sending now!!  its says "The operation could´t be completed. (MCMailErrorDomain error 1045)"

Help I need to work today!!

Apple THIS IS NOT FUN!

Try going to your mail preferences and re- typing your password on the otgoing smtp account.  That worked for me.

Try this:

1) Quit Mail

2) Go to users/Library/Mail/V3/MailData

3) Move all the files that named Envelope Index to the trash

4) Restart Mail

This will rebuild your entire mail index, you should be able to see all of your mail again.

Please tell me exactly how to get to this page pictured I am so lost

@RaNaeLucApple

IMPORTANT: The User’s Library folder (~/Library) is hidden by default since most people will not require access to it. It is hidden for your own safety as it is an important folder. Don’t reveal or make any changes to this folder if you are not entirely confident as to what you’re doing.

To reveal it:

1. go to FINDER

1. Open your home folder (this looks like a house) (/Users/yourusername) in the Finder. Depending on your Finder settings, this may be as easy as simply opening a new Finder window. Otherwise, choose Home from the Finder’s Go menu (Go > Home); or pressShift-Command-H.

Still in the Finder, choose View > Show View Options (or press Command-J).

• Near the bottom of the  View-Options palette is a setting called Show Library Folder. Enable this option. Your Library folder is immediately visible.

Close the View-Options palette.

• Library is now visible.  Click  folder library and you will see a list of other folders as shown below, then look for folder MAIL (highlighted below)

Click folder Mail, you will see two folders marked V2 and V3

Just follow what Eric Root said (scroll up this thread), i found MAIL DATA inside the V3 folder.  Delete files marked Envelope (i deleted all of those starting with Envelope, I think 3.  Then restart mail, it will take a few minutes but i got mine working.

I hope this helps.  By the way, if you have a problem sending, i just went to mail preferences and re typed my password in the outgoing SMTP account,

Perhaps some consolation:

I had the same problem, and re-indexing eventually worked. But before I did that, I was able to recover some of the "lost" email by searching for it in Spotlight. So if you're looking for a particular message, Spotlight might turn it up.

Yep, same problem. I've re-indexed. I think all my messages are retrieved, but all (2300) sit in the archive folder. I have lost ALL of the mailboxes I had created and managed my emails in. They don't exist anywhere (I searched in Finder for them). El Capitan is rubbish. What am I to do?

Well, it seems to be sorted now. Seems that it needed a bit of waiting...Annoyance has gone away now...

I can't take any credit but this worked for me:

Don't fret! Same thing happened to me. Go to Mail > Preferences > Accounts, and then uncheck the "Enable this account" option and then re-check it. Your folder structure should be restored.

Thanks, this was very helpful for me to find my Library