This may not take place in newer versions of CS-Cart but I’m running 3.0.2.
I recently added a SSL certificate to my site and now the hyper-links for the second e-mail for download of the product is HTTP and not HTTPS. I would like to know what file I need to make changes to in order to have the links work.
Many thanks in advance if you can assist. 
Okay, so I finally figured out how to do it! If anyone else is having this issue it is simple to correct if you know the location to look.
In CS-Cart Admin Panel:
Select Design → Template Editor
Now select the skin name that you are using.
Now select mail
finally select orders.
If you wish to modify the invoice that is being mailed to the customer you may do that by editing order_notification.tpl
If you wish to change the hyper-link text from http to https in an e-mail for automatic downloads open edp_access.tpl
so for a quick look at the location using the basic skin it would be Template Editor: skins/basic/mail/orders/ and one of the files mentioned above. I hope that information will be helpful to anyone that is facing the same problem that I've been facing!!