Flags and Smart Mailboxes not working well after Big Sur update!

Same problem here. Both the mail Search functionality and the "Smart Mailbox" feature is affected. Sometimes the search and/or Smart Mailboxes work after logging in and a quick logout/login helps.

Potential Solution

I noticed, that search results are found again (including Smart Mailboxes) if I rebuild the mailboxes. I cannot yet say how long this will stay ok, but so far it looks good.

1. Select one or multiple mailboxes
2. If you have many mailboxes arranged in folders, option click on the top-level to quickly expand the entire structure and then select as many as you like
3. Use Menu "Mailbox" / "Rebuild"
4. wait
5. Should be ok immediately after mail is done, but quitting/reopening should not harm either.

After weeks of problems (Flags and Smart Mailboxes not working, daily kernel panics, frequent beach balling, etc.) I may have resolved the issue.

Disk Utility's First Aid would complete successfully but had the these unresolved warnings:

warning: MT mapping (0x400000d63278a -> 0xf37667, 157, C) is not completely referenced
warning: MT mapping (0x40000136b4859 -> 0xc286d4, 20, C) is not completely referenced
warning: MT mapping (0x400001ea80f21 -> 0x12a4ac1, 94, C) is not completely referenced
The volume /dev/disk1s2 appears to be OK.
Storage system check exit code is 0.

Operation successful.

I finally resorted to the following drastic process.

1. Transferred most documents to either iCloud Drive, OneDrive, or DropBox
2. Verified two backups (just in case)
3. Booted in Recovery Mode
4. Launched Terminal in Recovery Mode and reset the Fusion Drive
5. Reinstalled macOS Big Sur
6. Reinstalled applications (and re-registered and configured)
7. Checked for and installed software updates
8. Restored documents not in a cloud repository
9. Restored some, but not all, settings documents from backup

Since going through the above process Big Sur has been much more stable. Several days now without a kernel panic and only a couple of beach balls.

I installed the Big Sur 11.2 update last night without incident.

I suspect that the problem may have been something with the original Fusion Drive set-up which was performed by Mojave.

The original formatting version info:

The volume Macintosh HD was formatted by storagekitd (1677.50.1) and last modified by apfs_kext (1677.60.23).

The volume Macintosh HD - Data was formatted by newfs_apfs (945.200.84) and last modified by apfs_kext (945.275.9).

New formatting version info:

The volume Macintosh HD was formatted by storagekitd (1677.60.23) and last modified by apfs_kext (1677.81.1).

Disk Utility no longer shows info for the "Macintosh HL - Data" volume.

Hope this helps someone.

Broken for me, too.

Above Steps did help for a SHORT time. Problem persists, even after updating to 11.2. VERY disappointed, that Apple is not prioritising this.

Something is definitely amiss in Big Sur's Mail.

Often when I select a flag in the sidebar the flag will disappear. If I wait for a bit it sometimes comes back but in some cases it only returns after restarting Mail.

Smart Mailboxes also seem to be broken. Selecting a smart mailbox often seems to do nothing - the list of messages just shows the mailbox you were viewing before you selected the smart mailbox. If I wait long enough, several minutes in some cases, the smart mailbox contents will sometimes appear.

Big Sur 11.0.2 please.