I’d recommend temporarily deactivating all plugins and see if that fixes the issue. If so, you will want to activate each plugin individually until you find the culprit(s). However, if the issue persists then you could try changing the theme and then go back to Customize. If neither of those worked, then it’s possible there is something on the backend causing issues with the URLs, such as odd rewrite rules.
Hey Tyler, I had no plugins installed. But I found the problem, instead of deleting index.html, I had deleted index.php and so it wasn’t registering it. I then reverted the file and it was fine.