Index: src/includes/admin/tools.php
===================================================================
--- src/includes/admin/tools.php	(revision 5341)
+++ src/includes/admin/tools.php	(working copy)
@@ -288,18 +288,19 @@
 		10 => array( 'bbp-sync-forum-visibility',    __( 'Recalculate private and hidden forums',             'bbpress' ), 'bbp_admin_repair_forum_visibility'         ),
 		15 => array( 'bbp-sync-all-topics-forums',   __( 'Recalculate last activity in each topic and forum', 'bbpress' ), 'bbp_admin_repair_freshness'                ),
 		20 => array( 'bbp-sync-all-topics-sticky',   __( 'Recalculate the sticky relationship of each topic', 'bbpress' ), 'bbp_admin_repair_sticky'                   ),
-		25 => array( 'bbp-group-forums',             __( 'Repair BuddyPress Group Forum relationships',       'bbpress' ), 'bbp_admin_repair_group_forum_relationship' ),
-		30 => array( 'bbp-forum-topics',             __( 'Count topics in each forum',                        'bbpress' ), 'bbp_admin_repair_forum_topic_count'        ),
-		35 => array( 'bbp-forum-replies',            __( 'Count replies in each forum',                       'bbpress' ), 'bbp_admin_repair_forum_reply_count'        ),
-		40 => array( 'bbp-topic-replies',            __( 'Count replies in each topic',                       'bbpress' ), 'bbp_admin_repair_topic_reply_count'        ),
-		45 => array( 'bbp-topic-voices',             __( 'Count voices in each topic',                        'bbpress' ), 'bbp_admin_repair_topic_voice_count'        ),
-		50 => array( 'bbp-topic-hidden-replies',     __( 'Count spammed & trashed replies in each topic',     'bbpress' ), 'bbp_admin_repair_topic_hidden_reply_count' ),
-		55 => array( 'bbp-user-topics',              __( 'Count topics for each user',                        'bbpress' ), 'bbp_admin_repair_user_topic_count'         ),
-		60 => array( 'bbp-user-replies',             __( 'Count replies for each user',                       'bbpress' ), 'bbp_admin_repair_user_reply_count'         ),
-		65 => array( 'bbp-user-favorites',           __( 'Remove trashed topics from user favorites',         'bbpress' ), 'bbp_admin_repair_user_favorites'           ),
-		70 => array( 'bbp-user-topic-subscriptions', __( 'Remove trashed topics from user subscriptions',     'bbpress' ), 'bbp_admin_repair_user_topic_subscriptions' ),
-		75 => array( 'bbp-user-forum-subscriptions', __( 'Remove trashed forums from user subscriptions',     'bbpress' ), 'bbp_admin_repair_user_forum_subscriptions' ),
-		80 => array( 'bbp-user-role-map',            __( 'Remap existing users to default forum roles',       'bbpress' ), 'bbp_admin_repair_user_roles'               )
+		25 => array( 'bbp-sync-all-reply-positions', __( 'Recalculate the reply position of replies',         'bbpress' ), 'bbp_admin_repair_reply_menu_order'         ),
+		30 => array( 'bbp-group-forums',             __( 'Repair BuddyPress Group Forum relationships',       'bbpress' ), 'bbp_admin_repair_group_forum_relationship' ),
+		35 => array( 'bbp-forum-topics',             __( 'Count topics in each forum',                        'bbpress' ), 'bbp_admin_repair_forum_topic_count'        ),
+		40 => array( 'bbp-forum-replies',            __( 'Count replies in each forum',                       'bbpress' ), 'bbp_admin_repair_forum_reply_count'        ),
+		45 => array( 'bbp-topic-replies',            __( 'Count replies in each topic',                       'bbpress' ), 'bbp_admin_repair_topic_reply_count'        ),
+		50 => array( 'bbp-topic-voices',             __( 'Count voices in each topic',                        'bbpress' ), 'bbp_admin_repair_topic_voice_count'        ),
+		55 => array( 'bbp-topic-hidden-replies',     __( 'Count spammed & trashed replies in each topic',     'bbpress' ), 'bbp_admin_repair_topic_hidden_reply_count' ),
+		60 => array( 'bbp-user-topics',              __( 'Count topics for each user',                        'bbpress' ), 'bbp_admin_repair_user_topic_count'         ),
+		65 => array( 'bbp-user-replies',             __( 'Count replies for each user',                       'bbpress' ), 'bbp_admin_repair_user_reply_count'         ),
+		70 => array( 'bbp-user-favorites',           __( 'Remove trashed topics from user favorites',         'bbpress' ), 'bbp_admin_repair_user_favorites'           ),
+		75 => array( 'bbp-user-topic-subscriptions', __( 'Remove trashed topics from user subscriptions',     'bbpress' ), 'bbp_admin_repair_user_topic_subscriptions' ),
+		80 => array( 'bbp-user-forum-subscriptions', __( 'Remove trashed forums from user subscriptions',     'bbpress' ), 'bbp_admin_repair_user_forum_subscriptions' ),
+		85 => array( 'bbp-user-role-map',            __( 'Remap existing users to default forum roles',       'bbpress' ), 'bbp_admin_repair_user_roles'               )
 	);
 	ksort( $repair_list );

@@ -1152,6 +1189,44 @@
 }

 /**
+ * Recalculate reply menu order
+ *
+ * @since bbPress (rXXXX)
+ *
+ * @uses wpdb::query() To run our recount sql queries
+ * @uses is_wp_error() To check if the executed query returned {@link WP_Error}
+ * @uses bbp_get_reply_post_type() To get the reply post type
+ * @uses bbp_update_reply_position() To update the reply position
+ * @return array An array of the status code and the message
+ */
+function bbp_admin_repair_reply_menu_order() {
+	global $wpdb;
+
+	$statement = __( 'Recalculating reply menuu order &hellip; %s', 'bbpress' );
+	$result    = __( 'Failed!', 'bbpress' );
+
+	// Post types and status
+	$rpt = bbp_get_reply_post_type();
+
+	// Get an array of reply id's to update the menu oder for each reply
+	$replies  = $wpdb->get_results( "SELECT `ID` FROM `{$wpdb->posts}` WHERE `post_type` = '{$rpt}';", OBJECT_K );
+
+	// Recalculate the menu order position for each reply
+	if ( ! empty( $replies ) ) {
+		foreach ( $replies as $reply ) {
+			bbp_update_reply_position( $reply->ID );
+		}
+	} else {
+		return array( 1, sprintf( $statement, $result ) );
+	}
+
+	// Cleanup
+	unset( $replies, $reply );
+
+	return array( 0, sprintf( $statement, __( 'Complete!', 'bbpress' ) ) );
+}
+
+/**
  * Recaches the private and hidden forums
  *
  * @since bbPress (r4104)
