Change Custom Post Type slug

The register_post_type_args filter can be used to modify post type arguments:

add_filter( 'register_post_type_args', 'wpse247328_register_post_type_args', 10, 2 );
function wpse247328_register_post_type_args( $args, $post_type ) {

    if ( 'portfolio' === $post_type ) {
        $args['rewrite']['slug'] = 'stories';
    }

    return $args;
}