Child theme not overriding 'includes' folder on server - on localhost it does

I have includes/setup.php on my parent theme, which I successfully override in child theme with includes/setup.php file on localhost development environment.

When I move the files to live server, the file is not overridden. The child theme is active, because css and all the files on child theme root are loaded, but includes/setup.php is not.

What might cause this?