yes, you are right about $args :/ I’ve removed the child code for the time being. The child messages show if you chose the option to show each email rather than email thread. I have gone back to only showing email thread which resolves the issue.

I now have the following code but am still seeing the unread hidden messages being included in the count.

        $this->loader->wp_add_filter('fep_message_query_args', array(
            $this->fep,
            'cmdu_hide_message'
        ), 10, 2);

        $this->loader->wp_add_filter('fep_message_count_query_args', array(
            $this->fep,
            'cmdu_hide_message'
        ), 10, 2);

    public function cmdu_hide_message($args, $user_id)
    {
        
        // Admin users can see all
        if (! current_user_can('administrator')) {           
            $args['post__not_in'] = $this->hide_mes_id();
        }
        
        return $args;
    }

And inside private function hide_mes_id()

        $not_post = array();
        foreach ($findrefs as $ref) {
            array_push($not_post, $ref->mes_id);
            
            /*
             * $child_args = array(
             * 'post_parent' => $ref->mes_id,
             * 'post_type' => 'any',
             * 'numberposts' => - 1,
             * 'post_status' => 'any'
             * );
             * $children = get_children($child_args);
             *
             * foreach ($children as $child) {
             *
             * array_push($not_post, $child);
             * }
             */
        }
        return $not_post;