This sounds similar to: Best method to cancel order after refund. Basically, if you refund an open order, it will not automatically close. You’ll need to use the API to cancel the fulfillment to remove it from the POS at this time.
As for your latter question: you can find refunds in the Orders API (each refund creates a new Order object with a refund and the source_order_id). I’m not sure what you mean by removing items from the order…I don’t think this is possible as we typically do not allow you to edit a paid-for order other than to change its status.