Reindex category products index at first and then execute following sql-script.

UPDATE `catalog_category_entity_int` AS `status`
INNER JOIN `eav_attribute` AS `attr` ON `attr`.`attribute_code` = 'is_active'
AND `attr`.`entity_type_id` = 3
AND `status`.`attribute_id` = `attr`.`attribute_id`
SET `status`.`value` = IF((SELECT COUNT(`index`.`product_id`)
	FROM `catalog_category_product_index` AS `index`
	WHERE `index`.`category_id` = `status`.`entity_id` GROUP BY `index`.`category_id`) > 0, 1, 0)
WHERE `status`.`store_id` = 0