The new Klarna payments app integration for Shopify provides integrated order management. Order management for Klarna orders should continue to be processed as part of your standard order management within your Shopify admin.
(While order management could be done directly via the Klarna merchant portal, this will cause Klarna data and Shopify order data to be out of sync and could result in unintended updates, e.g. duplicated refunds. Unless there is a problem, all order management should be done through the Shopify admin, not the Klarna merchant portal.)
Based on the "Payment capture" configuration (in the Shopify store admin, under Settings -> Payments), Klarna orders will either be automatically captured when placed OR the merchant will have to manually capture each order. (Note: this "Payment capture" setting applies to ALL orders in a Shopify store.) With this new payments integration, Klarna capture is no longer correlated to when the Shopify order is shipped (as was previously able to be done for the HPSDK integration).
Refunds made in Shopify (all types of Shopify refunds: before or after Shopify order fulfillment, full or partial refunds, order line based refunds or amount based refunds) will update the Klarna order after a short time delay of a few minutes (less than 10 minutes).
For orders that are not automatically captured (based on your store's Payment capture setting), Klarna recommends manually capturing the order prior to the Klarna order expiration date (that expiration time frame depends on your Klarna contract, e.g. 28 days). The Klarna order's authorization time cannot be extended within the Shopify admin; Klarna orders may possibly be extended in the Klarna Merchant Portal, if applicable for the order.