Below is what I think is relevant section of letsencrypt log, what seems strange here is the sites available.conf does not seem to be updated and the “already enabled redirect for this vhost” lines.
2018-08-28 22:56:53,836:DEBUG:certbot.storage:Creating directory /etc/letsencrypt/archive.
2018-08-28 22:56:53,836:DEBUG:certbot.storage:Creating directory /etc/letsencrypt/live.
2018-08-28 22:56:53,837:DEBUG:certbot.storage:Archive directory /etc/letsencrypt/archive/mysite.com and live directory /etc/letsencrypt/live/mysite.com created.
2018-08-28 22:56:53,837:DEBUG:certbot.storage:Writing certificate to /etc/letsencrypt/live/mysite.com/cert.pem.
2018-08-28 22:56:53,837:DEBUG:certbot.storage:Writing private key to /etc/letsencrypt/live/mysite.com/privkey.pem.
2018-08-28 22:56:53,837:DEBUG:certbot.storage:Writing chain to /etc/letsencrypt/live/mysite.com/chain.pem.
2018-08-28 22:56:53,838:DEBUG:certbot.storage:Writing full chain to /etc/letsencrypt/live/mysite.com/fullchain.pem.
2018-08-28 22:56:53,838:DEBUG:certbot.storage:Writing README to /etc/letsencrypt/live/mysite.com/README.
2018-08-28 22:56:53,847:DEBUG:certbot.plugins.selection:Requested authenticator webroot and installer apache
2018-08-28 22:56:53,850:DEBUG:certbot.cli:Var authenticator=webroot (set by user).
2018-08-28 22:56:53,854:DEBUG:certbot.cli:Var installer=apache (set by user).
2018-08-28 22:56:53,869:DEBUG:certbot.storage:Writing new config /etc/letsencrypt/renewal/mysite.com.conf.
2018-08-28 22:56:53,871:DEBUG:certbot.reporter:Reporting to user: Congratulations! Your certificate and chain have been saved at:
/etc/letsencrypt/live/mysite.com/fullchain.pem
Your key file has been saved at:
/etc/letsencrypt/live/mysite.com/privkey.pem
Your cert will expire on 2018-11-26. To obtain a new or tweaked version of this certificate in the future, simply run certbot again with the "certonly" option. To non-interactively renew *all* of your certificates, run "certbot renew"
2018-08-28 22:56:53,884:INFO:certbot_apache.configurator:Created an SSL vhost at /etc/apache2/sites-available/mysite.com-le-ssl.conf
2018-08-28 22:56:53,896:DEBUG:certbot.reverter:Creating backup of /etc/apache2/sites-available/mysite.com-le-ssl.conf
2018-08-28 22:56:53,974:INFO:certbot_apache.override_debian:Enabled Apache socache_shmcb module
2018-08-28 22:56:54,199:INFO:certbot_apache.override_debian:Enabled Apache ssl module
2018-08-28 22:56:54,516:INFO:certbot_apache.configurator:Deploying Certificate to VirtualHost /etc/apache2/sites-available/mysite.com-le-ssl.conf
2018-08-28 22:56:54,517:INFO:certbot_apache.override_debian:Enabling available site: /etc/apache2/sites-available/mysite.com-le-ssl.conf
2018-08-28 22:56:54,759:INFO:certbot_apache.configurator:Deploying Certificate to VirtualHost /etc/apache2/sites-available/mysite.com-le-ssl.conf
2018-08-28 22:58:11,062:WARNING:certbot_apache.configurator:Added an HTTP->HTTPS rewrite in addition to other RewriteRules; you may wish to check for overall consistency.
2018-08-28 22:58:11,119:DEBUG:certbot.reverter:Creating backup of /etc/apache2/sites-enabled/mysite.com.conf
2018-08-28 22:58:11,142:INFO:certbot_apache.configurator:Redirecting vhost in /etc/apache2/sites-enabled/mysite.com.conf to ssl vhost in /etc/apache2/sites-available/mysite.com-le-ssl.conf
2018-08-28 22:58:11,143:DEBUG:certbot_apache.configurator:Already enabled redirect for this vhost
2018-08-28 22:58:11,364:DEBUG:certbot.reporter:Reporting to user: If you like Certbot, please consider supporting our work by:
Donating to ISRG / Let's Encrypt: https://letsencrypt.org/donate
Donating to EFF: https://eff.org/donate-le
Here is my sites available .conf file, its the second RewriteEngine on directive that had to be added manually.
# Default virtual host config for mysite.com
<VirtualHost *:80>
ServerName www.mysite.com
ServerAlias mysite.com
DocumentRoot /srv/www/mysite.com
<Directory /srv/www/mysite.com>
Options +FollowSymLinks
AllowOverride All
Require all granted
RewriteEngine on
RewriteBase /
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php?q=$1 [L,QSA]
</Directory>
RewriteEngine on
RewriteCond %{SERVER_NAME} =mysite.com [OR]
RewriteCond %{SERVER_NAME} =www.mysite.com
RewriteRule ^ https://%{SERVER_NAME}%{REQUEST_URI} [END,NE,R=permanent]
</VirtualHost>