I have not run into this problem before, so I'm not sure what all is causing it, and every topic I've found on the matter hasn't explained much, so here goes.
In WordPress' backend, I've been making changes to the code via the Theme Editor. Whenever I make a change to any other .php file, it updates and shows when I refresh the site. However, the Main Index Template (index.php) instead only was showing
<?php //Silence is golden. ?>, despite the fact that the file on the server has information on it, and I can see all the layout and information on the main page, front-end wise. And when I copied and pasted the actual code into the main index file and modified it, it still didn't make anything change. The only way I'm able to change anything currently on the index file is by dropping the altered version in via FTP.
As I said, the other files all work correctly, and I can even alter the index.php pages in the Theme Editor for other themes, but not the one I'm currently working on.