Sounds more like certbot problem to me. You can also try updating certbot to the latest but no guarantee it'll work.
It didn't. I'm going to end up doing a manual renewal of the various certs, then migrate to a new install.
The problem is in /server/lib/classes/system.inc.php in public function create_relative_link($f, $t) the command $to = realpath($t);changes /etc/letsencrypt/live/DOMAIN/privkey.pemto /etc/letsencrypt/archive/DOMAIN/privkey7.pemNow symlinks are created to the archive of let's encrypt instead to live directory. On renewal of a certificate by certbot the number in the certfiles are increased and the symlink from /etc/letsencrypt/live/ to /etc/letsencrypt/archive/ are updated from this point the symlinks in /var/www/DOMAIN/ssl link to the wrong file. A workaround ist to change the /server/lib/classes/system.inc.php old: $to = realpath($t);new: if (strstr($f,'/etc/letsencrypt')) { $from = $f; } else { $from = realpath($f); }A better solution would be to change public function request_certificates($data, $server_type = 'apache') in /server/lib/classes/letsencrypt.inc.php to not use create_relative_link($f, $t). The line if(strstr($to,'/etc/letsencrypt/archive/')) $to = str_replace('/etc/letsencrypt/archive/','/etc/letsencrypt/live/',$to);in /server/lib/classes/system.inc.php in public function create_relative_link($f, $t) is not used.
Fixed by https://git.ispconfig.org/ispconfig/ispconfig3/commit/9ceff3c13b9dbace5b4ee9acae2b76c8611fc603
This problem came to me from nowhere and solution from above worked! I found my letsencrypt.inc.php and system.inc.php in /usr/local/ispconfig/server/lib/classes/ under CentOS 7.6, then replaced them with ones from Croydon's post and rebooted server. Thank you! There was one catch though - I deleted /etc/letsencrypt/live/{domain} hoping it will be recreated before found this thread and /var/log/letsencrypt/letsencrypt.log gave me errors so after replacing .php files I had to delete /etc/letsencrypt/renewal/{domain} too.
Instead of replacing libs in an old version with the ones of the current version, better update to the whole installation to the current ISPConfig version.
Yes, of course! Missed the last update, my bad. Updated to the latest 3.1.14p1 using Code: ispconfig_update.sh with default choices. Everything works just perfect. Thanks, Till!