This sql snippit updates the usage count of taxonomy terms.
UPDATE `wp_term_taxonomy` JOIN (SELECT `term_taxonomy_id`,count(*) as `new_count`,`count` as `old_count` FROM `wp_term_relationships` JOIN `wp_term_taxonomy` USING (`term_taxonomy_id`) GROUP BY `term_taxonomy_id`) as term_counts USING (`term_taxonomy_id`) SET `count` = `new_count` WHERE `old_count` != `new_count`