Missing emails in Mavericks mail app

After another day's investigation, I have tracked down what seems to be the cause of my missing emails. They were all in two separate email accounts that were linked to the same user name and web site. One was to an email account I had on the site, the other to my personal domain hosted by the same company. Both are POP accounts. That worked in Snow Leopard (10.6) Mail, but Mavericks Mail the emails in both accounts either disappeared entirely, or were blank when opened. When I opened either account in preferences to edit, Mavericks mail would say there was an error, which clued me in to the fact that it couldn't tell the two apart. As far as I can tell, that was the problem. When I deactivated one account this morning, all the email reappeared, and it's been stable now for most of the day. Two other POP accounts, one at gmail and one at Verizon, were not affected and have been stable.

You might check to see if you have two similar accounts.

I've been having problems with disappearing e-mails also. It has resulted in some serious upset with some of my customers who send me e-mails and expect a reply from me. It happens several times a week. I've tried rebuilding, restarting, and everything else recommended in this thread.

I'm running OS X Mavericks 10.9.5 - the latest update. All of my accounts are POP3. None of them are linked to the same account as they are each for a different company I either own or contract to.
I did finally, after considerable frustration, figure out today what's happening. The e-mails aren't actually lost. They're getting moved to other mail folders where I don't expect to find them. For example, I had a customer e-mail me with some information late yesterday. I replied back to the e-mail advising the customer I would work on the issue this morning. When I went to the mail folder for that customer this morning, the e-mail was gone. I finally found it in the "Sent" folder buried as part of a Conversation. But the conversation belongs in the customer's mail folder and it isn't there. Curiously, if I disable "Conversation Mode" the e-mail disappears from the "Sent" folder and cannot be found in the correct mail folder either. Thus, I know the e-mail is still in my machine but not being properly handled by Apple Mail.

Come on Apple, you can do better than this! It has been a year since the release of Mavericks and you still don't have Mail working to where it is useable, at least in a corporate environment. I'm about ready to dump Apple Mail and use Outlook for Mac.

Problem seem to exist also in El Capitan Public Beta 2, disappearing emails.. not good... p.s if Apple are listening some icons and colour would be a great addition to mail, is so plain and lacking appeal (see airmail, nice but also lucking function)

I thought I was losing my mind - emails disappearing out of thin air. Glad to know if wasn't just me. It is only the gmail ones that seem to be disappearing. So so so disappointing. I would have thought they would have a fix for this by now... the update yesterday didn't resolve this issue.

I thought the same too - I have spent hours on the phone to Apple Support and have now lost my patience with them because they totally deny it is happening and are blaming every other service provider for the issue and are failing to take responsibility for a software problem. It reminds me a bit of Volkswagen emissions scandal - perhaps Apple will have to recall all the faulty computers at a huge cost. I have two Apple computers both purchased mid 2012. My son purchased one last year. He has not been experiencing these problems so they may have fixed it in the newer versions but not in my version. I will not be buying any more Apple products as they are burying their head in the sand with this one and are failing to even acknowledge the problem exists let alone fix it. VERY DISAPPOINTED - I am no longer an Apple supporter.

I am thinking the same too - I have spent hours on the phone to Apple Support and have now lost my patience with them because they totally deny it is happening and are blaming every other service provider for the issue and are failing to take responsibility for their software problem. It reminds me a bit of the Volkswagen emissions scandal - perhaps Apple will have to recall all the faulty computers at a huge cost. I have two Apple computers both purchased mid 2012. My son purchased one last year. He has not been experiencing these problems so they may have fixed it in the newer versions but not in my version. I will not be buying any more Apple products as they are burying their head in the sand with this one and are failing to even acknowledge the problem exists let alone fix it. VERY DISAPPOINTED - I am no longer an Apple supporter.

I've had this problem twice. The first time was at least a year ago. Apple Support looked for a problem and eventually said I should check with my email host (GoDaddy). I did, they saw the problem and did a reset and sync. Problem solved. My disappearing emails started happening again this week and I just now called GoDaddy. They immediately saw the problem and did a reset and sync. So, at least my problem, and possibly yours, is with your email host and not Apple Mail. Before I called GoDaddy, I did a quick web search to see if there were possibly any other solutions with Apple Mail and found this thread. Since there was not a satisfactory answer in the thread, after I got the same answer from GoDaddy this second time, I thought I'd let you know my solution.

Hey guys, What was lost is now found!!!! All copies of my sent mail "disappeared". I have 4 yahoo mail accounts. But now they are found! All my sent mail from 1 July 2015 to 30 January 2016 have been "deleted" from my "Mailboxes" "Sent" mail box for all four accounts BUT a new FOLDER "Sent Messages" has been created as a separate folder in the Mailbox List under each respective account (you need too scroll don the mailbox list column) and the messages, and only for this period have been 'saved' to this new folder respectively!!! LOL!!

Hello, my problem as been solved by installing ClickToFlash. Had to do with adobe flash. By blocking

that I'm back to normal. Immediately changed the whole process. Clicking Inbox and all messages

immediatley there now ; Sent too. In Safari, Click preferences, Get extensions, add clickToFlash.

Also, yesterday I added Ka-Block and it's working great on pop-up ads.

Dan

I had a surprise disappearance of a group of emails about three weeks ago. They are still on my phone, since they were recent. But I also have for many years had a backlog of thousands of emails kept for various reasons--as george fromeast boston said, it was a kind of chronicle of much of my work. Quite a few contained attachments which I would retrieve through the mail program. This week, everything before mid-June of this year suddenly disappeared. It is not stored on my mail provider server, so apparently the only copy was in my mail program. Even though I had those emails a few days ago, none of the time machine versions of my mail program have anything different from my current day's version. This is extremely frustrating, and from the sound of these comments in this thread, there's nothing to be done. Isn't there some shadow of these emails hanging around in memory that Apple could help us recover?