How are COGS refunded?

Manual COGS (product cost) are refunded on the day the refund was issued in Shopify. Not when the order was initially placed. 

It is important to note that only the product cost is refunded not the product shipping cost. 

The COGs refund process is as follows: 

1. All the cogs are recorded for every single order during the selected period. 
2. A second call is sent out to gather all the refunds, all items which were refunded, canceled, or partially refunded will reduce the cogs total as the products are assumed to be received back to the merchant. 
3. The cogs for each order are netted out with the refunds which were issued in the period selected

If on a refund, you would not like the COGS decreased. The setting can be changed on this page here