Q: smart mailbox problem with El Capitan

Back up all data before proceeding.

This procedure will unlock all your user files (not system files) and reset their ownership, permissions, and access controls to the default. If you've intentionally set special values for those attributes on any of your files, they will be reverted. In that case, either stop here, or be prepared to recreate the settings if necessary. Do so only after verifying that those settings didn't cause the problem. If none of this is meaningful to you, you don't need to worry about it, but you do need to follow the instructions below.

Step 1

If you have more than one user, and the one in question is not an administrator, then go to Step 2.

Triple-click anywhere in the following line on this page to select it:

sudo find ~ $TMPDIR.. -exec chflags -h nouchg,nouappnd,noschg,nosappnd {} + -exec chown -h $UID {} + -exec chmod +rw {} + -exec chmod -h -N {} + -type d -exec chmod -h +x {} + 2>&-

Copy the selected text to the Clipboard by pressing the key combination command-C.

Launch the built-in Terminal application in any of the following ways:

☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)

☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.

☞ Open LaunchPad and start typing the name.

Paste into the Terminal window by pressing command-V. I've tested these instructions only with the Safari web browser. If you use another browser, you may have to press the return key after pasting.

You'll be prompted for your login password, which won't be displayed when you type it. Type carefully and then press return. You may get a one-time warning to be careful. If you don’t have a login password, you’ll need to set one before you can run the command. If you see a message that your username "is not in the sudoers file," then you're not logged in as an administrator.

The command may take several minutes to run, depending on how many files you have. Wait for a new line ending in a dollar sign ($) to appear, then quit Terminal.

Step 2 (optional)

Take this step only if you have trouble with Step 1, if you prefer not to take it, or if it doesn't solve the problem.

Start up in Recovery mode. When the OS X Utilities screen appears, select

          Utilities ▹ Terminal

from the menu bar. A Terminal window will open. In that window, type this:

resetp

Press the tab key. The partial command you typed will automatically be completed to this:

resetpassword

Press return. A Reset Password window will open. You’re not going to reset a password.

Select your startup volume ("Macintosh HD," unless you gave it a different name) if not already selected.

Select your username from the menu labeled Select the user account if not already selected.

Under Reset Home Directory Permissions and ACLs, click the Reset button.

Select

           ▹ Restart

from the menu bar.

Please take these steps to delete the Mail "sandbox" folders.

Step 1

Back up all data.

Triple-click anywhere in the line below on this page to select it:

~/Library/Containers/com.apple.mail

Right-click or control-click the highlighted line and select

          Services ▹ Reveal

from the contextual menu.* A Finder window should open with a folder named "com.apple.mail" selected. If it does, move the selected folder—not just its contents—to the Desktop. Leave the Finder window open for now.

Restart the computer. Launch Mail and test. If the problem is resolved, you may have to recreate some of your Mail settings. Any custom stationery that you created may be lost. Ask for instructions if you want to preserve that data. You can then delete the folder you moved and close the Finder window.

Caution: If you change any of the contents of the sandbox, but leave the folder itself in place, Mail may crash or not launch at all. Deleting the whole sandbox will cause it to be rebuilt automatically.

Step 2

If Step 1 doesn't solve the problem, repeat with this line:

~/Library/Containers/com.apple.MailServiceAgent

*If you don't see the contextual menu item, copy the selected text to the Clipboard by pressing the key combination  command-C. In the Finder, select

          Go ▹ Go to Folder...

from the menu bar and paste into the box that opens by pressing command-V. You may not see what you pasted because a line break is included. Press return.

Do you use iCloud Drive? Do you have any other smart mailboxes? Have you tried to delete the smart mailbox and recreate it from scratch? If not, please do that now.

Please back up all data, then open the iCloud pane in System Preferences. If the box marked iCloud Drive is checked, click Options, then uncheck the box marked Mail and confirm. Your iCloud data should be preserved on Apple's servers.

Test to see whether there's an improvement, then re-check the box and test again. It may take a noticeable amount of time for your iCloud Drive data to resynchronize.

My previous comment was edited after posting.

It's not clear whether you followed the instructions in my last comment after I changed it.

What exactly are the filtering criteria for this mailbox?

Please create new ones as a test, each with only a single criterion that you use in the problem mailbox. Do those work?

Back up all data. Quit Mail if it's running.

Triple-click anywhere in the line below on this page to select it:

~/Library/Mail/V3/MailData

Right-click or control-click the highlighted line and select

          Services ▹ Open

from the contextual menu.* A folder window should open. From that folder, move the following files to the Desktop:

          SmartMailboxesLocalProperties.plist

          SyncedSmartMailboxes.plist

Test. If Mail now works, delete the files you moved. Otherwise put the files back where they were, overwriting any that may have created in their place.

*If you don't see the contextual menu item, copy the selected text to the Clipboard (command-C). In the Finder, select

          Go ▹ Go to Folder...

from the menu bar and paste into the box that opens by pressing command-V. You may not see what you pasted because a line break is included. Press return.