Q: El Capitan dowloaded now have lost emails

Try re-indexing the mailboxes. This can take awhile if you have a lot of mail.

Reindex messages

You are welcome

I am trying to solve the same problem.  the only file I have in V2 is Accounts.plist.  There is nothing else.  Are there updated instructions for re-indexing?

I have just downloaded El Capitan and all of my mail accounts have disappeared. Now even Mail itself won't open. I tried the re-indexing but no such folder exists. Help, please.

Try looking in V3 for MailData.

I found the files mentioned in the V3 directory and removed the three of them that were listed as Envelope Index. Once I launched mail, it began the indexing process and the number of messages it was importing was approximately the number I had prior to upgrading to El Capitan. However, once Mail completed indexing the emails, none of the lost messages showed up in the Mailbox.

I've also rebuilt the mailbox and still can't get the messages to appear. Help

Thanks Eric. All found now!

Any advice for recovering my Sent mail on a POP account? I upgraded to El Capitan this morning and Mail didn't migrate any of my Sent mail over for my work account, which is a POP email account.

Just Upgraded to El C. and all  my "on my mac" sub mailboxes have disappeared too.  All the tricks mentioned in this thread tried, but no luck.  Any ideas?

Unfortunately the did not work for me. All my mailboxes are intact except the Inbox is empty .  .  .  and I cannot send mail .  .  . I get a message that says "

This message could not be sent. It will remain in your Outbox until it can be sent. This message could not be sent because your account does not have a preferred outgoing mail server. Select an outgoing mail server from the list below." Of course, there is no "list below". Very disappointed with what should be a simple install in a latest-model MacBook Pro. Been a Mac user since 1988 and every update seems to break something these days

Thank God for this, it was a hair raising experience when I upgraded to El Capitan on my Imac and found all my emails gone, (inbox, all folders, sent).  Indexing currently in progress. I hope I am able to recover everything.

This happened to me too but the message says MCMailErrorDomain error 1032, so I went to mail preference and then re-typed my password again on the smtp account.  It seemed to have worked as I was able to send however everything is gone, but I am trying the re-indexing at the moment and hopefully I can recover them.

I have this same problem. I have 4 different business emails on pop accounts. I have lost all my emails.

Tried looking for these "index" files in V2 and V3 but they are not there.

I need to recover these soon!! Apple folk this is a nightmare!!

This is for Apple folk:

I am gonna post a message on my Facebook to tell people not to upgrade until this can be fixed... its a colossal waste time spending ages trying to recover mails that you had in your mail..

Its the equivalent of someone coming into your house and taking or "hiding" all your files and important documents and not telling you where everything is...