Automatic issuing (PRO)
You may set automatic issuing documents (invoices and proforma invoices) upon reaching the specific WooCommerce order status (It's possible to choose more than one). You can speed that process by changing the status for more orders through Bulk Actions in the WooCommerce -> Orders Screen.
Read more about both settings in Invoice Settings, Proforma Settings, and Correction Settings.
Issuing Corrections (PRO)
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.
You may also issue documents manually on the WooCommerce orders screen with the Invoice Action buttons and inside each order.
Read more about manual issuing proforma and invoices and manual issuing corrections.