I just took the time to recode it all... I figured you wouldn't be able to do much about it anyway, and it showed the file as blank when I opened it once so it was just completely gone.. I have no idea what happened, it was because of switching themes for some reason.I'm seeing an active index.php file with content in it; did you reupload it recently?
I've not heard of a case where changing anything in cPanel would wipe your index.php file as well, as it's not modifying any files inside public_html whenever you change settings. The only thing that should be able to wipe it is if you edit it via file manager.