UPDATE entity_map, folders join
(
 SELECT MIN(id) id ,(LOWER(TRIM(name))) name
  FROM folders
  GROUP BY (LOWER(TRIM(name)))
) AS f1 ON ((f1.id <> folders.id) AND (f1.name=folders.name))
SET entity_map.folder_id=f1.id
WHERE folder_id=folders.id;

DELETE FROM folders
 USING folders LEFT JOIN entity_map ON (folders.id=entity_map.folder_id)
 WHERE entity_map.folder_id IS NULL;