Using advanced custom fields, if you know what the shortcode is and what you want to replace it with you can do so with the following.

	$site_url = get_site_url();
	$field = get_field('template_html');
	$field = str_replace("[url]", $site_url, $field);
	echo $field;

you could also use this with another shortcode using the following, replacing $site_url for $shortcode_val

$shortcode_val = do_shortcode('[some_other_shortcode]');