After upgrading to el capitan, all of my sent email has been deleted.

This did not work for me either. I have several email accounts. Only one had this issue. What's really odd is I had one new item in my inbox and after I selected 'rebuild', that got deleted as well. The account in question was a POP account that I've had for about 15 years and never had a migration issue until now.

Now it's back to finding all my lost emails in my backup. Fortunately, this isn't a huge problem as I try to keep my inbox fairly clean. When I finish something that the email pertains to, I file it. However, I have a ton of clients that have hundreds of emails in their inbox and don't file regularly. This update will be a disaster since many conduct their business through their email. I'm having to send an alert to all my clients letting them know NOT to upgrade to El Capitan.

Works with sent mailbox if you do it again while sent mail is active, (click on it before you do the procedure again).

The sent mailbox isn't the issue. Anything that was in a folder, even the sent folder, was preserved. It was on the inbox and only on one account. I've tried a few options to 'rebuild' it, but nothing shows up. If I happen to have something in the inbox, it gets removed as well and is not stored elsewhere, it just vanishes. I've sent test messages from an outside account to test this and it's pretty consistent in what's happening.

When I upgraded to El Capitan this morning, on re-start I discovered that the whole of my Mail was wiped out. Accounts, messages, mailboxes, everything has gone!

I can't use "rebuild" as it is greyed out, in any case i haven't got any mailboxes to rebuild. I have tried going in to ~/library/mail/mail data/v3 and deleting all the "envelope index" files and then restarting Mail, but nothing happens. I have a TM back up but that was last Friday.

Any more ideas or should I take my 2015 MacBook Pro to the local Apple Shop..........

G

Rebuild didn't work for me. Enter Time Machine while using Mail crashed Mail so that didn't work for me, either.

But eventually I got my Sent messages back by doing the following:

(Essentially I found the Time Machine backup of emails sent and imported back to Mail)

On Finder, go to Go, press Alt key so Library option shows up. Click on it.

Then go to Containers.

Then (scroll down to) com.apple.mail > Data > Library > (double click on) Mail

There should be V2 and V3 folders.

Click on the TimeMachine icon next to your Wifi or Speaker or Clock icon on the upper right hand corner.

Select "Enter Time Machine"

I went back to the time right before I upgraded to El Capitan. There was only V2 folder, no V3.

I expanded V2 folder. I saw my POP account and under it there was a "Sent Messages.mbox"

I highlighted it, right-clicked, and selected "Restore 'Sent Messages.mbox' to..." (to Desktop or a location easy to remember/find)

Back to Mail. Go to File > Import Mailboxes...

You'll see "Import data from:" select "Apple Mail", then "Continue"

Navigate to "Sent Messages.mbox" restored earlier. Highlight and click "Choose"

For me, all the sent emails were imported under Import / Sent Messages folder listed on the bottom left.

At this point, I can leave them there or drag them to the proper Sent folder.

My guess is somehow Sent messages got lost in the process of upgrading from V2 to V3.

I hope this helps.

There is no Rebuild in the Mailbox menu in my Mail program (version 9.0 - should be the latest I think!)

I had same problem, synchronising or rebuild has not recovered my inbox. I resorted to re-creating the original POPmail account in Mail and everything has been restored.

Thank you Ralph - this helped me a lot!

Amazing. This worked like a charm. I had the same problem, and spent a couple of hours on the phone with Apple (and it was still being looked into). After the upgrade, I lost everything in one account with more than 11,000 emails. And though it was backed up on Time Machine I was unable to get the backup to actually show a "restore" button. But this did it. Thank you - great advice!