Please be informed that Cpanel Let's Encrypt interface is going away.
The Let's Encrypt feature has now been integrated with AutoSSL.
Users that would like to manually run or check AutoSSL status on their domains, can now do this SSL/TLS Status Interface in the Cpanel.
Please see the steps below on how to install the Let's Encrypt SSL:
Locate the SSL/TLS Status link under the security section of your Cpanel
Click on "Run AutoSSL"
Go to the domain and click on "View Certificate"
Scroll down on the view certificate page and click on install