If Automatic Corrections are enabled then Corrections will be issued to every refunded order but only if there is an issued invoice for an order and no refunding took place.
Any correction of the amount on the invoice should be done in the same way. Go to the order you want to adjust and to the product list, then click Refund.
Under the net amount and VAT of products, appears edit fields to enter the sums of refund. Both amounts must be entered manually, which means that with partial refunds for the product, you must calculate the amount of VAT refunded on the basis of the net amount.
After completing the fields, click Refund ... manually or process the refund through the payment gateway (if available).
Then, update the order, so the Invoice Correction will appear in the existing Invoice Box.
You may also check out the free plugin to let customers send refund requests in WooCommerce.