bp_messages_screen_conversation_mark_notifications()

function bp_messages_screen_conversation_mark_notifications() {
	global $thread_template;

	/*
	 * Only run on the logged-in user's profile.
	 * If an admin visits a thread, it shouldn't change the read status.
	 */
	if ( ! bp_is_my_profile() ) {
		return;
	}

	// Get unread PM notifications for the user.
	$new_pm_notifications = BP_Notifications_Notification::get( array(
		'user_id'           => bp_loggedin_user_id(),
		'component_name'    => buddypress()->messages->id,
		'component_action'  => 'new_message',
		'is_new'            => 1,
	) );
	$unread_message_ids = wp_list_pluck( $new_pm_notifications, 'item_id' );

	// No unread PMs, so stop!
	if ( empty( $unread_message_ids ) ) {
		return;
	}

	// Get the unread message ids for this thread only.
	$message_ids = array_intersect( $unread_message_ids, wp_list_pluck( $thread_template->thread->messages, 'id' ) );

	// Mark each notification for each PM message as read.
	foreach ( $message_ids as $message_id ) {
		bp_notifications_mark_notifications_by_item_id( bp_loggedin_user_id(), (int) $message_id, buddypress()->messages->id, 'new_message' );
	}
}