Rachel here from the Shopify Guru Team!
Yes, you can refund a specific line item for a product from your admin. When you go into the order and click Refund, you have the option to choose how many of each line item you'd like to refund.
This tutorial will guide you through the steps: Refund part of an order
I hope this helps, but if you have any further questions - be sure to reach out to Shopify Support!