Smart Mailbox not filtering

Select all of the mailboxes in the sidebar and use the Mailbox ➙ Rebuild menu option. Let it run for about 30 minutes. Close and open Mail and see if the filtering is OK.

If the above doesn't help try this: How to rebuild the Spotlight index on your Mac - Apple Support  and test again.

Hi again. Let's give it another go. Try booting into the Recovery volume (boot with the Command + R keys held down  - Intel Macs) or  (How to Boot an Silicon Mac into Recovery Mode) and reinstalling the system. It will not affect your user data but you should always have a full and current backup before installing any system updates or upgrades.

🤞

It might be time to make an appointment at the nearest   Apple Genius Bar or Apple Authorized Service Provider and have them go thru it with a fine tooth comb.

If you do make sure you have a full and current backup of your boot drive with Time Machine or whatever backup app you use.

Addendum: there is one more thing you can try: with Mail closed search the Mail/V10 folder for any file that contains "envelope" in its file name. Move them to the Trash bin and relaunch Mail. You can use the shareware app Find Any File to do the search.

Any files with the envelope in the file name can be dragged from the search results window to the Trash bin.

FAF can search areas that Spotlight can't like invisible folders, system folders and packages.  

Mail will reload all of the emails back into the various albums and the smart albums will take a bit to repopulate. Be sure to keep your 🤞.

At least the Mini will be easy to carry in if that's the way you go. I had to take an iMac in and that's no walk in the park.

Do you have a lot of smart mailboxes? If not you might try deleting them, rebuilding all of the mailboxes again and then recreate the smart mailboxes.

I have a problem with a smart mailbox that reports two unread messages when there are none. I've tried what I've suggested to you with no success. So I brushed up on my addition and subtraction and mentally calculate what should be in the smart album. 😔

So including the Trash might be you best bet until another update comes out to see it it is fixed.

I rebuilt the Spotlight index for the Mail folder in ~Library/Mail. Rebooted the MacMini and no change in the Smart Mailbox behavior - still requires the "Include Messages from Trash" box to be checked in order to function properly.

Can you search Spotlight for BJKeppel and it returns Mail messages correctly? Make sure Mail & Messages is selected in the Spotlight System Settings.

Boot into Safe Mode according to How to use safe mode on your Mac and delete from there.

Note:  if you have a wireless keyboard with rechargeable batteries connect it with its charging cable before booting into Safe Mode.  This makes it act as a wired keyboard as will assure a successful boot into Safe Mode.

FAF can search areas that Spotlight can't like invisible folders, system folders and packages.  

Spotlight (Finder Search) can find all of those just fine. You have to know how to configure the search, but it is not impossible. Search Everywhere - Apple Community

Curious if the genius bar came up with a solution...?