The command is: /usr/local/bin/certbot-auto --install-only otherwise certbot-auto would try to configure certs in apache on its own which then breaks ISPConfig.
Run those commands shown in your error for details on what the problem is. You can probably also get them from running 'apachectl configtest'. You may have more bad vhost files you need to fix (eg. temporarily remove), or ??
I'm sorry but I don't understand what you mean What problem did you see? and how do I fix it? Do you mean to remove every domain appears under /etc/apache2/sites-enabled/ when this error appears "AH00526: Syntax error on line 121"
Basically yes. The error is that there is still a LetsEncrypt certificate used in these files. That is why before deleting the certificates you should deactivate the "LetsEncrypt" checkbox in ISPC. Because you missed that, you get these errors. So for every domain where you have deleted the certificate and did not deactivate it in ispc before, you will get this error. The solution is do delete the web in sites-enabled. Then this web will not be started. Then, when Apache is running again, you bring back LetsEncrypt and reactivate one web after the other with LetsEncrypt.
I guess the main problem is that he used certbot on the shell with the apache module, files with -le-ssl.conf in the name are a clear indication for that, and this must break the systems s ispconfig is not able to manage these sites anymore due to the duplicated config. So all files with -le-ssl.conf in their name where the domain is managed in ISPconfig has to be removed anyway to get a working system back.
After few deletes Apache started again. but even though I check SSL and Letsencrypt boxes, they uncheck themselves also the sites show the Apache default page
Ok, that's a good starting point. Have a look at the Let's encrypt FAQ to find out why you can't activate LE in a site now: https://www.howtoforge.com/community/threads/lets-encrypt-error-faq.74179/
Αnd the last problem was solved I made this change and everything works again. "- When your server is behind a NAT router so that the server itself can not reach the hosted domains, then enable the option "Skip Letsencrypt check" under System > Server config > web." Thank you all for help.