By default, Hide My WP Ghost adds the rewrite rules in 2 places in .htaccess to avoid errors when other plugins are deleting the rules from .htaccess.
If you want to have the Hide My WP Ghost rewrite rules only inside the #BEGIN HMWP_RULES … #END HMWP_RULES add this line in the wp-config.php file.
define( 'HMW_RULES_IN_WP_RULES', false );
Save the settings in Hide My WP > Change Paths and the plugin will remove the rewrite rules from WordPress definition #BEGIN WordPress …. #END WordPress