Before posting :
7f2dd95b-5c4d-4013-820c-42ca9263efa6-image.png
Right after manual cert renewal :
86f8b0a5-1058-43d1-844a-2c70ee1ac91c-image.png
You saw the date/time change ?
The concerned
<cert>
....
<crt> ........</crt>
.....
</cert>
in the config.xml showed me the cert was changed thus saved to config.xml
How could pfSense otherwise use the new certificate dater a reboot ?
Because it's in the config.xml .... (and no where else).
Btw :
a397d082-d42c-478b-b7fc-0eae9ab12b7b-image.png
edit : I tend to say : read the log from /tmp/acme/<your domain>/acme_issuecert.log and you have your answer why it was not renewed and thus why it wasn't written to config.xml and why it didn't doesn't show in System > Certificate Manager > Certificates
Edit : See the official video : https://www.netgate.com/resources/videos/lets-encrypt-on-pfsense.html => 49 minutes and 30 seconds ;)