As of July 17, any changes made to a Shopify invoice (total or partial cancellation of charges) will generate a Credit Note. Credit Notes can be viewed and downloaded from the Billing section of the admin.
Credit Notes will have an associated refund mechanism: 1) refund to the original payment method; OR 2) Shopify Account Credits. Shopify Account Credits are post-bill credits that can only be applied to charges on future invoices.