Вот решение:
Проблема заключалась в пересечении идентификаторов в таблицах заказов, поэтому magento перепутал все элементы.
Решено это с усечением всех таблиц заказов:
TRUNCATE sales_order
;
TRUNCATE sales_order_datetime
;
TRUNCATE sales_order_decimal
;
TRUNCATE sales_order_entity
;
TRUNCATE sales_order_entity_datetime
;
TRUNCATE sales_order_entity_decimal
;
TRUNCATE sales_order_entity_int
;
TRUNCATE sales_order_entity_text
;
TRUNCATE sales_order_entity_varchar
;
TRUNCATE sales_order_int
;
TRUNCATE sales_order_text
;
TRUNCATE sales_order_tax
;
TRUNCATE sales_order_varchar
;
TRUNCATE sendfriend_log
;
TRUNCATE tag
;
TRUNCATE tag_relation
;
TRUNCATE tag_summary
;
TRUNCATE wishlist
;
TRUNCATE log_quote
;
TRUNCATE report_event
;
TRUNCATE sales_flat_quote
;
TRUNCATE sales_flat_quote_address
;
TRUNCATE sales_flat_quote_address_item
;
TRUNCATE sales_flat_quote_item
;
TRUNCATE sales_flat_quote_item_option
;
TRUNCATE sales_flat_quote_payment
;
TRUNCATE sales_flat_quote_shipping_rate
;
TRUNCATE sales_flat_order_item
;
ALTER TABLE sales_order
AUTO_INCREMENT = 1;
ALTER TABLE sales_order_datetime
AUTO_INCREMENT = 1;
ALTER TABLE sales_order_decimal
AUTO_INCREMENT = 1;
ALTER TABLE sales_order_entity
AUTO_INCREMENT = 1;
ALTER TABLE sales_order_entity_datetime
AUTO_INCREMENT = 1;
ALTER TABLE sales_order_entity_decimal
AUTO_INCREMENT = 1;
ALTER TABLE sales_order_entity_int
AUTO_INCREMENT = 1;
ALTER TABLE sales_order_entity_text
AUTO_INCREMENT = 1;
ALTER TABLE sales_order_entity_varchar
AUTO_INCREMENT = 1;
ALTER TABLE sales_order_int
AUTO_INCREMENT = 1;
ALTER TABLE sales_order_text
AUTO_INCREMENT = 1;
ALTER TABLE sales_order_tax
AUTO_INCREMENT = 1;
ALTER TABLE sales_order_varchar
AUTO_INCREMENT = 1;
ALTER TABLE sendfriend_log
AUTO_INCREMENT = 1;
ALTER TABLE tag
AUTO_INCREMENT = 1;
ALTER TABLE tag_relation
AUTO_INCREMENT = 1;
ALTER TABLE tag_summary
AUTO_INCREMENT = 1;
ALTER TABLE wishlist
AUTO_INCREMENT = 1;
ALTER TABLE log_quote
AUTO_INCREMENT = 1;
ALTER TABLE report_event
AUTO_INCREMENT = 1;
ALTER TABLE sales_flat_quote
AUTO_INCREMENT = 1;
ALTER TABLE sales_flat_quote_address
AUTO_INCREMENT = 1;
ALTER TABLE sales_flat_quote_address_item
AUTO_INCREMENT = 1;
ALTER TABLE sales_flat_quote_item
AUTO_INCREMENT = 1;
ALTER TABLE sales_flat_quote_item_option
AUTO_INCREMENT = 1;
ALTER TABLE sales_flat_quote_payment
AUTO_INCREMENT = 1;
ALTER TABLE sales_flat_quote_shipping_rate
AUTO_INCREMENT = 1;
ALTER TABLE sales_flat_order_item
AUTO_INCREMENT = 1;