I migrated to Shopify with “Clear current data on Target Cart” option but some of orders weren’t deleted. Why?

Due to technical peculiarities of Shopify, orders where payment was processed through Shopify POS or your online checkout cannot be deleted. Thus, when migrating to Shopify with “Clear current data on Target Store” additional option enabled, some of the orders might not be deleted by Cart2Cart.

All the other data existing in your Target Shopify store will be wiped out though.