Index: wp-content/plugins/handbook/handbook.php
===================================================================
--- wp-content/plugins/handbook/handbook.php	(revision 7417)
+++ wp-content/plugins/handbook/handbook.php	(working copy)
@@ -330,7 +330,9 @@
 	}
 
 	function pre_get_posts( $query ) {
-		$query->is_handbook_root = false;
+		if ( $query->is_main_query() && ! property_exists( $query, 'is_handbook_root' ) ) {
+			$query->is_handbook_root = false;
+		}
 
 		if ( $query->is_main_query() && ! $query->is_admin && ! $query->is_search && $query->is_post_type_archive( $this->post_type ) ) {
 			// If the post type has a page to act as an archive index page, get that.