chartディレクトリ内の記事が404エラーになる

I don’t speak or read Japanese so apologies if google translate didn’t do a good job.

But I think the problem you describe is the M Chart post_type slug conflicting with an existing one in your install of WordPres.

You can override slugs and any other post type arguments using the following filter hook:

register_post_type_args

In practice this looks something like this:

add_filter( 'register_post_type_args', 'm_chart_register_post_type_args', 10, 2 );

/**
 * Filter register_post_type_args and modify it for our purposes
 */
public function register_post_type_args( $args, $post_type ) {
	if ( 'm-chart' == $post_type ) {
		$args['rewrite']['slug'] = 'something-other-than-chart-here';
	}

	return $args;
}

This should work as is if you throw it into your functions.php file and change the something-other-than-chart-here to what you’d prefer M Chart to use instead of chart for individual chart URLs.