Mail messages missing...

With Mail quit....

Go to the User's Library folder. This folder is hidden by default. To unhide: Select the Finder in the Dock. Under Go in the Menu bar > hold down the Option key and you’ll see the Library.

• Go to Containers. Drag the com.apple.mail folder to the Desktop

• Go to Mail folder.

Select the V4 > MailData folder.

Delete any files in MailData with envelope in the name. (should be 3)

Open Mail. It will reindex your files.

Let me know if this resolves your issue.

I have the same problem. I ditched El Capitan because of Mail issues, among others.

I am certainly willing to go back to Yosemite because Apple can't get something as basic as email right.

Setup a new account, see if the problem's global, or just related to your account...

CREATE A NEW USER

Go to System Preferences --> Create a New User in Users & Groups.

Switch to the New User by logging out/in or use Fast User Switching.

You can skip signing in with your Apple ID unless you want to test any iCloud features.

Only default Apple apps will be in the Dock in the new User. Go to Applications to open other apps you might want to test.

Do you still see the issue?

If yes, then the problem is with your base files.

If no, then the problem is in your User's folder.

The problem exists in all user folders. I created a test user account and it exists there,

I have moved back to Yosemite.

I suggest that you create a new partition for testing Sierra before making a full move to Sierra when you do decide to upgrade again.

Sorry you are having a bad experience. I did a clean install and have had no issues with Mail.

I suggest you only add back one account to test after you do the reinstall.

Even if you don't use iCloud email, it's a good quick email account to test.

Add only one account at a time and verify that it's working correctly before adding any other accounts.

Command-L. Or View -> Disable Filter

Doing a clean install is not always required. Often it's a better option because the user has many years of installing over the base system.

You mentioned "Are you listening Apple?"... If you want Apple to hear your complaint, send feedback. This forum is a user to user support system. Not a way to communicate with Apple.

http://www.apple.com/feedback/macosx.html

This fixed the issue for a user we have. Some mailboxes, including sent items, had a filter applied so were showing no mail even though we could see in webmail the items were there (menu bar at top was reporting 0 filtered results)

Turned off filters and all mail was visible again. The filter is applied per mailbox folder, so you have to select each mailbox and then click View - > Disable Filter (or Command-L) for every folder where the messages are hidden.

Strangely, these filters were brought across from a clean install of Sierra and re-add the google mail account. Same behavior before and after the clean install.

Thanks for this.

Thanks!!! I knew I pressed smth like that 🙂 could not find it in the menus myself

Really helpful, thanks. Fell into this trap by accidentally enabling the filter (Command-L) when I was trying to de-flag a message (Command-shift-L).

try this: view->disable message filter