Steps to reproduce:

1. Keep the default thread view of the message list
2. Receive a new email on a message where you have many threaded messages
3. Check the content of the notification that appeared
4. Try to find that new message, on first sight

Actual results:

1. The notification says something about a message that the user can find only if she expands the right thread.
2. While collapsed (default), the date sorting/order is incoherent

Expected results:

1. The last message should be shown while a thread is collapsed in Message list
2. The Date sorting/order should be always right, coherent

This is especially important in Supernova, as Message thread becomes the default

This is more complicated than it looks since the way threads are right now are organized by first received message, which turned into the thread parent.
It's not currently possible to "change the order" of threaded messages unless we rebuild the database to be a real global indexed DB, which we're already doing but it's deferred for after 115. Bug 1572000 if you're interested in following the work.

This is not related to the supernova UI, so I'm removing the flags and setting the blocker.

This might actually be related to the JS implementation of IMAP. I've just seen on one of my accounts that email is received but does not appear in the list.

Check the Error console for any error messages that look like they're IMAP related.

Once you've done that, in the config editor (bottom of the general tab of preferences), try toggling mailnews.imap.jsmodule to false and then restarting Thunderbird, and try again to see if it clears the issue.

If that is the case, I suspect this is related to one of the bugs blocking bug 1707547.