Thank you for the fast reply [rg305]!
We did restart the Dovecot service (as well as postfix and Apache) and even rebooted the server but all to no avail.
As mentioned, before we did certbot with --preferred-chain "ISRG Root X1", we got the levels of Certificate Chain with DST Root CA X3 at the third level.
After doing certbot --preferred-chain "ISRG Root X1", there are now two levels in the Certificate Chain with ISRG Root X1 at the second level.
But when the issuer line of the openssl s_client -connect out still shows this:
issuer= O = Digital Signature Trust Co., CN = DST Root CA X3
Before --preferred-chain "ISRG Root X1":
root@server2:/# openssl s_client -connect server2.example1.com:993 -servername server2.example1.com
CONNECTED(00000003)
depth=3 O = Digital Signature Trust Co., CN = DST Root CA X3
verify error:num=10:certificate has expired
notAfter=Sep 30 14:01:15 2021 GMT
Certificate chain
0 s:/CN=server2.example1.com
i:/C=US/O=Let's Encrypt/CN=R3
1 s:/C=US/O=Let's Encrypt/CN=R3
i:/C=US/O=Internet Security Research Group/CN=ISRG Root X1
2 s:/C=US/O=Internet Security Research Group/CN=ISRG Root X1
i:/O=Digital Signature Trust Co./CN=DST Root CA X3
After we did the above steps 1 and 2, we got this
After --preferred-chain "ISRG Root X1":
root@server2:/# openssl s_client -connect server2.example1.com:993 -servername server2.example1.com
CONNECTED(00000003)
depth=3 O = Digital Signature Trust Co., CN = DST Root CA X3
verify error:num=10:certificate has expired
notAfter=Sep 30 14:01:15 2021 GMT
Certificate chain
0 s:/CN=server2.example1.com
i:/C=US/O=Let's Encrypt/CN=R3
1 s:/C=US/O=Let's Encrypt/CN=R3
i:/C=US/O=Internet Security Research Group/CN=ISRG Root X1
But mysteriously, today the issuer of the openssl s_client out is now correct ISRG Root X1.
Yesterday:
root@server2:/# openssl s_client -connect server2.example1.com:993 -servername server2.example1.com
CONNECTED(00000003)
depth=3 O = Digital Signature Trust Co., CN = DST Root CA X3
verify error:num=10:certificate has expired
notAfter=Sep 30 14:01:15 2021 GMT
Certificate chain
0 s:/CN=server2.example1.com
i:/C=US/O=Let's Encrypt/CN=R3
1 s:/C=US/O=Let's Encrypt/CN=R3
i:/C=US/O=Internet Security Research Group/CN=ISRG Root X1
root@server2:/# openssl s_client -connect server2.example1.com:443 -servername server2.example1.com
CONNECTED(00000003)
depth=3 O = Digital Signature Trust Co., CN = DST Root CA X3
verify error:num=10:certificate has expired
notAfter=Sep 30 14:01:15 2021 GMT
Certificate chain
0 s:/CN=server2.example1.com
i:/C=US/O=Let's Encrypt/CN=R3
1 s:/C=US/O=Let's Encrypt/CN=R3
i:/C=US/O=Internet Security Research Group/CN=ISRG Root X1
Today:
root@server2:/# openssl s_client -connect server2.example1.com:993 -servername server2.example1.com
CONNECTED(00000003)
depth=2 C = US, O = Internet Security Research Group, CN = ISRG Root X1
verify return:1
depth=1 C = US, O = Let's Encrypt, CN = R3
verify return:1
depth=0 CN = server2.example1.com
verify return:1
Certificate chain
0 s:/CN=server2.example1.com
i:/C=US/O=Let's Encrypt/CN=R3
1 s:/C=US/O=Let's Encrypt/CN=R3
i:/C=US/O=Internet Security Research Group/CN=ISRG Root X1
root@server2:/# openssl s_client -connect server2.example1.com:443 -servername server2.example1.com
CONNECTED(00000003)
depth=2 C = US, O = Internet Security Research Group, CN = ISRG Root X1
verify return:1
depth=1 C = US, O = Let's Encrypt, CN = R3
verify return:1
depth=0 CN = server2.example1.com
verify return:1
Certificate chain
0 s:/CN=server2.example1.com
i:/C=US/O=Let's Encrypt/CN=R3
1 s:/C=US/O=Let's Encrypt/CN=R3
i:/C=US/O=Internet Security Research Group/CN=ISRG Root X1
So everything is fine now but we don't know what happened. Maybe some caching somewhere? Thank you once again Rudy.