Problem

I've created a smart mailbox in macOS Mail for "Unread" messages with the following rules:

Contains messages that match all of the following conditions:

• Message is in the mailbox: Inbox
• Message is unread

The smart mailbox will always correctly include unread messages in my inbox. But often, it will incorrectly include read messages in my inbox. Any ideas on how I can fix this?

Other information and troubleshooting steps so far

• Currently using macOS Sierra 10.12.6
• Email account is hosted by Google
• Other smart mailboxes with other rules still work properly.
• If I use the filter button in my inbox, Mail will properly perform filtering -- even for unread messages.
• I tried marking the problematic messages as unread and then as read again. Afterwards, the number next to the title of the "Unread" mailbox will decrease (because I have taken steps to mark messages as read), but the "Unread" mailbox itself will still list those messages (even though they are read).
• I tried the above step from gmail.com. Same result.
• I tried getting new mail. Nothing changes. I tried rebuilding my mailboxes. No rebuilding happens.
• I tried rebooting my computer in safe mode. Then, any smart mailbox I created would contain no messages regardless of the rules I set.
• There doesn't seem to be any pattern to which messages are problematic.
• My "Unread" smart mailbox still behaves properly for non-problematic messages even if it contains problematic messages.
• Once a problematic message appears in my "Unread" smart mailbox, it will stay there for a few days. Then, it will suddenly leave "Unread" and sit in my Inbox where it belongs.

Solution 1:

Spotlight is responsible for searches, so I would add your home folder to the spotlight system preference privacy settings.

• Then say Ok to any prompts that mention search will break.
• Then remove your home folder and let the indexer re-index mail messages.
• Restart after 30 minutes if you don’t see an improvement

There are more drastic and questionable options, but let’s start with safe and easy.