Phantom messages in Mail

Interesting and Déjà vu. 5 days ago this started happening on my Macbook Pro running El Capitan 10.11.6. I hope that they have another fix that "Improves the accuracy of unread counts in Mail" 😉. I tried rebuild, reboots, etc. My count is accurate for the mail folder, but my smartbox for new mail shows 23 emails. 😟

Fixed the problem. Looking back, the rebuild actually did reduce my count on phantom mail in the "New Mail" smartbox by 10. These 10 were in the pop mail folder that I had rebuilt. The rest were in a "On My Mac" "Other mail" folder. There wer to the same account but were located on my "On My Mac" "Other Mail" folder. This folder is for mail that I receive from people that are not in my contacts list so I separate the "new and junk" from the mail I get from friends.

So, I had an idea and created another "On My Mac" folder called "fix mail". I took the items that were showing as not read (but were) in my "New Mail" smart mailbox and dragged them into "fix mail". The new mail counter dropped from 23 to 0. I then dragged them back into "Other mail" folder and deleted the "fix mail" folder. My rationale, and some of the experts may agree is that the items, though from my pop mail account, were not rebuilt as they were "On My Mac". When I moved them, the index was updated with the proper status.

It was actually a pretty simple fix, once figured out. 🙂

I hope this may help others if they happen to have the problem and the email is actually in an "On My Mac" folder.

Not particularly helpful, but I'm seeing the same two problems: my Flagged count shows as 9 though in fact there are 2 flagged messages, and my Unread smart mailbox always shows a count of 1 more than the actual number of unread messages.

I am having the same issue. And phantom emails in my Unread Mail smart mailbox. I removed the "Envelope" files from the library as was suggested, and which caused a complete rebuild of my emails, all 42,000 of them. Seemed to help some. But still have 2 emails showing in my Unread mailbox, but none there. Also, the 3 Envelope files that I put in the trash cannot be emptied from the trash. Get a message saying they are currently in use.

Lastly, the Junk Mail filter is not doing it's job. I'm getting a bunch now that will not filter to the Junk mail folder.

All in all, a pretty flawed release, IMHO.

I, too, upgraded to Mavericks and now have false indicators in my 'Flagged' folder under 'Mailboxes' in the sidebar (supposedly 3 emails flagged Red, 1 Green, and 1 Blue—but I have no flagged messages). I tried rebuilding all my mailboxes, but no change.

Other ideas?

Another "me too" post. My message counts seem to be completely screwed up on two different Macs with Mavericks. Mailboxs (gmail specifically) show unread messages where there are none, and flagged message count is completely wrong. The badge on the dock icon reflects the same bad unread message count.

The bogus unread message counts are different on two Macs. iOS and Web don't show any unread messages at all, and it wasn't happening before Mavericks. I've flagged everything on the accounts involved as "read"

Same problem here I have 23 red flagged messages according to the flag count but none are there. Is there a fix yet?

I've had this same problem, and the following worked for me, but it's a bit hazardous so make sure you have a backup of all your Mail messages, if you keep them locally, first.

1) Quit Mail.

2) In Finder, press Shift-Comand-G, and in the "Go to the folder:" box, enter:

~/library/mail/V2/maildata

3) Drag the following files to the Trash:

Envelope Index

Envelope Index-shm

Envelope Index-wal

ExternalUpdates.storedata

ExternalUpdates.storedata-shm

ExternalUpdates.storedata-wal

FlagMailboxes.plist

4) Start Mail; it should tell you it needs to reimport all your Mail messages; allow it to do so.

When this process is complete, you may see Flagged messages are once again indicated, but this time when you select the Flagged mailbox you should see the messages Mail thinks are flagged, and you should be able to take whatever action you want on those messages (unflag, delete, etc.)

This actually fixed my issues on both Macs.

The only thing I would add is rebooting before restarting the Mail app, otherwise you won't be able to empty your trash.

Apple released an update today that claims to have fixed this issue. (I don't know for sure because I also followed William Kucharski's steps to fix my Mail woes.) See <http://support.apple.com/kb/HT6030?viewlocale=en_US&locale=en_US>.

Just upgraded to new update, re-booted OSX, relaunced Mail, and still showing that there are 2 unread emails in my Unread Mail smart mailbox, but no email showing. I even deleted the that folder and recreated it. Still shows 2.

It is an Apple suggested fix and it has solved this type of problem for many people.

Reindex messages

The fix suggested by William Kucharski is an older Apple-recommended fix. All it does is delete bad indexes and caches, forcing the Mail program to re-build them. If you follow the instructions- you won't cause any sort of harm to your Mac. I believe the Mavericks fix that came out will help prevent the bad message counts from happening to begin with, but if they are already bad- it may not fix them. After doing the recommended fix and updating Mavericks, all of my Google accounts seem to be working correctly now.