If you receive an email from WHM/Cpanel stating something similar to the following:

The SSL certificate for “ftp” on “server.example.com” will expire in less than 30 days.

Then you can do the following to regenerate the self-signed SSL certificate.

1. Log into WHM

2. Navigate to Home » Service Configuration » Manage Service SSL Certificates

3. Click on "Reset certificate" for the relevant service (Will usually have a warning icon next to it).

Once completed you will no longer receive the notification via email.