Open the order, click Refund, enter the amount, then choose the button that refunds via Clover. That sends the money back to the customer's card.
"Refund manually" only writes the refund into WooCommerce and deliberately does not touch the card — use it when you have already refunded some other way.
Partial refunds
Refunding part of an order with several items works: Clover will not part-refund such a payment directly, so the plugin refunds the matching lines of the Clover order instead. Refund the same line twice and Clover refuses, and the reason is shown on the refund screen.
Orders paid on the Clover device
An in-store sale imported into WooCommerce cannot be refunded from the website: Clover's ecommerce refunds only know online payments. Refund it on the Clover device; the plugin writes a note on the order reminding you.