Phantom messages in Mail

Worked for me! THEY'RE GONE!!

Well, not so fast. They appeared to be gone, but then one phantom started showing up in the counter of the Unread Mail Smart Mailbox. So I tried the whole process again. Again, 43,000+ emails reindexed. And still have one showing as unread in the counter, with nothing in the Smart Mailbox. One thing I did note this time. As I watched the window during the reindexing process, it counted up to the total number of messages, but stopped one short of total count shown. Would seem there is still a gremlin in there that this process, or the Apple Update, doesn't handle. Man this is frustrating!

I also went into Time Machine and it shows correctly, with no counter for the phantom message. Not sure what that means.

I too was having the phantom flag issues even with the updates, still there. I followed your instructions and deleted all the files... And my flag count went even higher and was still incorrect.

Just deleted all the files a second time ...... And now mail keeps hanging up & won't run the reindexing process, just get the beach ball of death 😟

I just tried William Kucharski's solution as well and now have the spinning ball of death as well. Have forced quit and restarted my computer a few times and am now on the phone with applecare. I wish I had read this page instead of just the page with Kuckarski's suggestion. I think I have to reinstall the OS ... on hold now for a senior advisor. So, although I do not know the fix yet I would advise not to follow the steps that Kucharski advised as a solution ... or prepare for your mail program to freeze when starting up.

Update: I have been on the phone with applecare, sent "upstairs" to two top tech people, and have sent a mail systems report given to a programmer specifically for the mail program. They will analyze the data and get back to me earliest on Monday (today is Saturday).

So ... I would strongly advise that you do not delete those files that Mr. Kucharski suggested and call applecare from the start if you have this problem.

I am fortunate in that I have everything backed up to Time Machine, a second mac, and on numerous drives. However, the mail program - at least for now - is DOA on my main computer and I have spent hours on the phone with tech at apple.

This was an email account problem for me -- not an iPhone problem.

I had a phantom email message problem -- all originating in a Yahoo email account. Went to the Yahoo account online. With advanced search, looked for all messages sent to my account address. Search found the exact number of emails that were incorrectly flagged on my iPhone. These were all junk emails received over a two year period, but not appearing in either the junk or trash folders -- for some reason invisible in the account. I marked all for deletion -- would not and could not be deleted normally. So went to the 'empty trash folder' command and they were removed. iPhone is now free of the 'unread' notifications.

Reminds me of occasional failure of Yahoo, Hotmail, Gmail accounts to delete sent/received messages despite settings calling for deletion after a set time period.

I hope this helps.

Same.

Just updated to 10.9.1 and the unread count in smart mailboxes continues being wrong. After re-indexing, the problem re-appears slowly. Quite frustrating. Are we really changing for good?

Continued to have a false count in my "In" smart mailbox. Had given up. Then all of a sudden a couple of days ago, it just disappeared and now shows correctly. Go figure.

10.9.2 was released today, and lists as one of the fixes "Improves the accuracy of unread counts in Mail". (See http://support.apple.com/kb/HT6114 for the full list). My own Mail was showing correct unread counts when I updated, so I don't know if updating would have fixed the problems I was having earlier.

But I'm still running 10.9.1. No update is currently showing as available.

It's probably rolling out in a somewhat staggered way. I checked for it an hour or so and it didn't show up then. Half an hour later I noticed a red badge on my App Store icon, and at that point the update was listed.

The servers were a bit overloaded; try again now.

I've just used William Kuckarski's advice and it seems to have worked fine. Thanks William.