Assuming you have followed the steps in the previous article to get your certificate, then you should be able to run this if your certificate is not expired.
cd /tmp/letsencrypt
sudo ./letsencrypt-auto renew


or to get a new certificate

sudo ./letsencrypt-auto -c /path/to/domain.com.ini -d domain -d www.domain.com auth

That may not happen if you have done fancy stuff on your website.

Expired

Google Chrome will not go to your website, so for troubleshooting use Firefox. Letsencrypt does not follow the same warnings that Google Chrome shows. It also does not care about HSTS headers.

You are going to have to reissue the certificate because renew will not work.

Document Root

If you are telling Apache that http://www.domain.com should just be http://www.domain.com/owncloud, then anything placed  on your server for letsencrypt will not be visible you need to temporarily disable that override.

Change DocumentRoot from /var/www/owncloud to /var/www

sudo vim /etc/apache2/sites-available/ownCloud-ssl.conf
sudo vim /etc/apache2/conf-available/owncloud-ssl.conf


Certificate Location

The following is the contents of my domain.com.ini file.

rsa-key-size = 4096
server = https://acme-v01.api.letsencrypt.org/directory
text = True
authenticator = webroot
agree-tos = True
renew-by-default = True
email = email@gmail.com
webroot-path = /var/www/html

Since I set webroot-path to /var/www/html, I need to create a logical link in /var/www/ to the .well-known directory so that the verification can work.

make logical link
cd /var/www
ln -s -T html/.well-known/ .well-known

Restart Server

You can do reload> or restart but both work.
sudo service apache2 restart