Whether you bought domain from godaddy or not. Whether either of your domains are hosted on godaddy or not but if you bought SSL from godaddy:-

  1. you got to go to My products in godaddy
  2. Go to SSL certificate, click manage on the domain you want to change from.
  3. click on the middle one, Rekey & Manage
  4. expand Change the site that your certificate protects and uncheck?Change to a hosted domain , type in your new domain name and off course, SAVE!!

5.Generate CSR using your server console or Cpanel ( Part of Installing SSL on ubuntu 16.04 apach2)

6. Submit all saved changes:-

7. It will take godaddy some time to generate SSL:-