Let's Encrypt ACME server doesn't and cannot know which cert was not renewed on purpose or which cert should be renewed.
Perhaps I'm being unclear. I understand that the ACME server can't know that -- that's what I contemplate communicating in an improved notification email message.
It appears that there are actually two certificates at play here -- let me call them "expiring certificate" and "newer certificate" -- each pertaining to the topmost domain name ("byron.zeetix.com" in this case). I think the ACME server knows of each of the expiring and newer certificates.
Here is some notification email text that I would find less confusing:
A certificate for byron.zeetix.com will expire in 9 days (on 21 Nov 22 15:36 +0000). A newer certificate for byron.zeetix.com (expiring on 15 Dec 22 18:16 +0000) has different domain names from the expiring certificate.
Visitors to your web site who use domain names not on the newer certificate may encounter errors.
Here are the domain names on the expiring certificate:
byron.zeetix.com
covid.tms.byron.zeetix.com
tms.byron.zeetix.com
wiki.byron.zeetix.com
zeewiki.byron.zeetix.com
Here are the domain names on the newer certificate:
byron.zeetix.com
covid.tms.byron.zeetix.com
fullstack.tms.byron.zeetix.com
tms.byron.zeetix.com
The remainder of the notification email is clear as-is.