Why is ca.san_config, ca.csr and letsencrypt files missing in conf directory?

[Richard G]

I just got an e-mail that an SSL certificate for a hostname would expire in 20 days which I found odd because it just renewed.
Seemed this was for an old hostname, but when using my script to check letsencrypt dates I found this:

cat: /usr/local/directadmin/conf/ca.san_config: No such file or directory
Lets Encrypt Hostname

-- Created: Fri May 14 00:15:01 CEST 2021 - 1620944101
-- Renewal: Tue Jul 13 00:15:01 CEST 2021
-- Renewal in 57 days.

So it looks the automatic renewal went fine 2 days ago, but the creation of the ca.san_config file was not.

Now I checked 2 other servers, and on one other server, also the ca.san_config was missing.

Now it seems on both servers where the ca.san_config was missing, there was more missing in the directadmin/conf directory.
The good one looks like this:

-rw-r----- 1 diradmin access   2.2K 2021-05-08 00:17 cacert.pem
-rw-r----- 1 diradmin access   5.9K 2021-05-08 00:17 cacert.pem.combined
-rw-r----- 1 diradmin access     11 2021-05-08 00:17 cacert.pem.creation_time
-rw-r--r-- 1 root     root     4.3K 2020-05-08 00:17 cacert.pem.new.tmp
-rw-r----- 1 diradmin access   1.7K 2020-05-08 00:17 ca.csr
-rw-r----- 1 diradmin access   3.2K 2021-05-08 00:17 cakey.pem
-rw-r----- 1 diradmin access   3.7K 2021-05-08 00:17 carootcert.pem
-rw------- 1 diradmin diradmin  155 2019-09-10 00:19 ca.san_config
-rw------- 1 diradmin diradmin 3.5K 2021-03-31 18:58 directadmin.conf
-rw------- 1 diradmin diradmin 3.2K 2019-09-10 00:19 letsencrypt.key
-rw-r--r-- 1 root     root     1.7K 2019-09-10 00:19 letsencrypt.key.json
-rw------- 1 diradmin diradmin 3.2K 2019-10-26 11:11 letsencrypt.staging.key
-rw-r--r-- 1 root     root     1.5K 2019-10-26 11:11 letsencrypt.staging.key.json
-rw------- 1 diradmin diradmin 1.6K 2021-04-19 04:01 license.key
-rw------- 1 diradmin diradmin 1.6K 2021-03-20 04:01 license.old
-rw------- 1 diradmin diradmin   51 2021-05-15 23:55 my.cnf
-r-------- 1 diradmin diradmin   40 2019-09-08 21:08 mysql.conf

From both servers missing the ca.csr and ca.san_config and all letsencrypt files are missing:

drwx------ 2 diradmin diradmin 4.0K 2021-04-20 04:01 .
drwxr-xr-x 7 diradmin diradmin 4.0K 2021-05-15 03:18 ..
-rw-r----- 1 diradmin access   2.2K 2021-05-14 00:15 cacert.pem
-rw-r----- 1 diradmin access   5.9K 2021-05-14 00:15 cacert.pem.combined
-rw-r----- 1 diradmin access     11 2021-05-14 00:15 cacert.pem.creation_time
-rw-r----- 1 diradmin access   3.2K 2021-05-14 00:15 cakey.pem
-rw-r----- 1 diradmin access   3.7K 2021-05-14 00:15 carootcert.pem
-rw------- 1 diradmin diradmin 3.3K 2021-03-31 18:59 directadmin.conf
-rw------- 1 diradmin diradmin 1.6K 2021-04-20 04:01 license.key
-rw------- 1 diradmin diradmin 1.6K 2021-03-21 04:01 license.old
-rw------- 1 diradmin diradmin   50 2021-05-09 00:50 my.cnf
-r-------- 1 diradmin diradmin   39 2021-03-13 18:19 mysql.conf

This makes me curious as all these servers were created the same way and I always create the hostname certificate manually.

How can this be fixed? Do I need to re-create the hostname certificates manually?
And if yes, why wasn't the ca.san_config and the letsencrypt files were created automatically?

Good server hostname renewal may 8th.
Bad servers renewal may 9th and may 14th.