migrated to new server

Hello, I am new here to this community and to Cpanel. I have taken on a volunteering project for a friend. His host had migrated to new servers and this required my friend to move all of his old web content to the new server. Now, he had 2 websites. Website 1, and Website 2. In the original setup, both websites had their own folder in the root directory: website1.com and website2.com. After moving his content to the new server space he had to create an addon domain. He did this in Cpanel. So he moved everything over, created the addon domain for website #2. Website #1 however, will not load! When browsing to website #1 he is taken to an index page that shows folder indexes of website1.com and website2.com. If he browses to website #2 then the webpage appears normally. Both websites have been designed with PHP and I suspect because of a line describing "DOCUMENT_ROOT", website#1 is not loading because the root folder for website1.com is the parent of both websites. When trying to change the .htaccess in this root directory I am able to redirect the visitory to website1's index.php, but the site does not load properly, again, because I suspect the DOCUMENT_ROOT is incorrect. To make it really easy, and maybe somewhat insane, my friend's content for website1 and website 2 is 1:1. same folder structure, same content. Any ideas where to go from here? Does the host need to change the root directory as website1.com should be pointed to website1's content folder where it's index.php is located?