Mail Smart Mailboxes and Flagged Mailboxes not working after update

I updated from most recent 26 directly to 27.0.1.

Prior to that, all my Smart Mailboxes worked. Not sure about the Flagged, as I don't usually view them, but I do always use my `unread` smart mailbox, and always check my `spam` smart mailbox. Worked before upgrade, failed consistently post.

Message filter is disabled. Never use it.

I do use mail rules. My mail rules appear to be functioning correctly.

I rebuilt the mailboxes. No change.

The only 'funny' thing I am doing is running SpamSieve, but it is working OK. It should not affect the way the Smart Mailboxes are working. They are simply a display filter used to select a set of messages.

I have changed the simple `unread` filter. It is `all of: message is unread and message is in inbox(s)`. I have deleted each of the two constraints one at a time, adding it back. At all times, there has been no resulting change as one would expect from the change. Also changed 'is unread' to 'is read'. All attempts result in empty 'smart' mailbox.

I just switched over to another login to see if it also had problems, but it was not logged in to its appleID, so no email was flowing. When I logged out of that session, it hung, and I had to `ssh` in and `pkill -9 loginwindow WindowServer`. This effectively logged out all users, and when I logged in to continue typing this (draft saved, thankfully) I observed that everything is working again in `Mail.app`. Same as some reddit thread noted.

So perhaps the 'secret' is to log out and in again (although make sure you can ssh in to recover from what appears to be another issue).

Replying to my own post:

I’ve done some more digging on this and found a couple of discussions about it.  One on here and one on Reddit.  Their conclusions about the problem seem, so far, to be correct.  It’s an iCloud problem.

I’ve had an iCloud/Mail/Smart-Mailboxes problem in the past, where one Mac (running an older OS) got completely stuck with its Smart Mailboxes that were in the Mail.app.  Every time I used this old Mac, other Macs would have deleted Smart Mailboxes reappear.  I couldn’t find any way to stop it happening.  So that was an iCloud issue and it seems to me now, that this problem is essentially the same.

iCloud Drive for Mail, essentially does one thing.  It syncs (or makes available) the Mail account-settings across multiple devices.  That’s all it does for Mail, so it’s of little importance.  So somewhere, it’s got a bug that is breaking Mail’s settings across devices.

It’s easily fixed by simply turning OFF Mail in iCloud Drive settings.  To do this go to:

System Settings / iCloud / Drive / Apps syncing to iCloud Drive / and Turn OFF Mail.

It’s been a couple of days now, but I notice my everyday Smart Mailbox ('Today') is updating instantly when I open Mail.  Looks very hopeful as a fix.

Based on the limited technical details provided and the fact that this started after the macOS 27.0.1 upgrade, the following is based primarily on Apple Support and Apple Developer documentation. 

The timing is relevant, but it does not by itself establish that the update is the cause.

Since both Smart Mailboxes and the Flagged mailbox have stopped working, I would start with a few simple checks. 

First, make sure Mail is receiving messages normally and that View > Filter > Disable Message Filter is selected. 

If you use Mail rules, it is also worth checking Mail > Settings > Rules, since filtering or rules can affect which messages appear. Apple Support — If you can't see email messages in Mail on Mac

Then, manually flag a message that should appear in the Flagged mailbox. 

Apple says that flagged messages should appear there. If the newly flagged message does not appear either, that would be a useful indication that the problem is affecting the Flagged mailbox itself. Apple Support — Mark emails to revisit later in Mail on Mac

Personally , I found Flagged email would not appear straight away , though , after completely closing Apple Mail application and opening Mail again. The Flagged email would appear 

If the messages are still present in their normal mailboxes but the Smart Mailboxes are not updating, try Mailbox > Rebuild on an affected mailbox. 

Apple recommends rebuilding when messages appear to be missing or searches do not return expected results. Apple Support — Create or delete mailboxes in Mail on Mac

There is also something particularly relevant in Apple's macOS 27 Developer Release Notes: 

Apple documented an issue where Smart Mailboxes might not update while Mail was being used. 

Apple subsequently listed that issue as resolved. That does not prove it is the cause of your 27.0.1 problem, but it is certainly relevant given when your problem began. Apple Developer — macOS 27 Release Notes

Have you already tried these checks, particularly manually flagging a new message and using Mailbox > Rebuild? The results should tell us what to investigate next.

What you are seeing looks much more like a Mail/macOS state problem following the upgrade to macOS 27.0.1 than a problem with the Smart Mailboxes themselves.

The timing is important. 

Your Smart Mailboxes worked normally before you upgraded directly from macOS 26, and afterward both Smart Mailboxes and Flagged Mailboxes stopped displaying messages. 

At the same time, your regular Mail rules continue to work, and SpamSieve appears to be working normally.

Your testing of the Unread Smart Mailbox is especially telling. You removed each condition separately, added it back, and even changed “is unread” to “is read.” 

Nothing changed, the Smart Mailbox remained empty regardless of the criteria. Rebuilding the mailboxes also made no difference. 

That makes a problem with the Smart Mailbox definitions themselves unlikely.

The most useful clue came from your last test: after logging out and back in, Mail.app started working normally again. 

That is a much stronger lead than the earlier troubleshooting. It shows that, in this instance, a complete macOS logout/login restored both the Smart and Flagged mailboxes.

So, if the problem happens again, I would try that before changing anything else: quit Mail, log out of macOS normally, log back in, and check the Smart and Flagged mailboxes.

I would not yet call this a confirmed macOS 27.0.1 bug, or say that logging out specifically “resets the Mail index.” 

We do not  know exactly what internal Mail or macOS state was causing the problem. 

What we do know is that the mailboxes stopped working after the upgrade and that logging out and back in restored them.

I would also keep the separate logout problem in its own category. 

The fact that the other user session hung during logout and required an SSH/pkill recovery is worth investigating as a separate macOS 27 issue, but I would not deliberately reproduce it just to fix Mail.

For now, I would leave the Smart Mailbox definitions, Mail rules, mailbox rebuilds, and SpamSieve configuration alone. 

Your testing has already given fairly good evidence that none of those is the obvious cause.

This has been happening for me for quite a while ( ~Sonoma?). In the past, I'd rebuild the mailboxes and it would be fine for quite a while, then would recur. With 27.0 it didn't happen, but with 27.0.1 it happened twice and now, disappointingly with 27.2 it's happened again.

I was hopeful that the reworked Spotlight in macOS27 would fix it... but no. If when it happens again, before doing anything else, you make a completely new simple Smart Mailbox as, e.g. 'Unread', you'll find that it doesn't work. Rebuilding the account/mailbox which contains an unread email works immediately for me. So it's a spotlight/indexing issue. For some reason it's breaking and of course, this affects Search/Find as well, although you may never notice that.

I've had this issue since updating to 27.0.1.

Logging out of the user and restarting seems to have resolved it

Replying to my own posts again…

Well, a few days later and nope, that’s not the answer.  It’s not a simple iCloud fix.  I’m back where I was.  Logouts/Restarts change nothing.  Rebuilding the Mailboxes seems to be the only fix.

What’s *very interesting* as I dig a little deeper into this, is that I’ve noticed that this bug goes further than Mail.app itself.  The App Switcher and the Dock both get it wrong too!

Mail app:

Dock:

App Switcher: