I have just been testing our new POS system before installation and have some issues regarding refunds and creating daily and weekly sales reports.
1 - Why are refunded items still appearing on the Sales figures?
This shouldn't be happening. The customer has been refunded so we no longer have their money.
2 - Is the only way to get accurate sales figures to export the Payment Method report and subtract the refunded amount from the total sales.
Look at discussion on POS forum. This is running issue and its not just a POS issue. Fundamentally Shopify will not remove the refunded unit from the Product reports unless after you refund it from POS then go to admin and cancel the order. I have written extensively on this topic at POS forum. For exchanges you also cannot refund part of the order since cancelling can only be done for entire order not partial. Therefore you have to refund the entire order and then process again what was not returned/exchanged but make sure you choose the same payment method as original order else your register closing will not balance across sources of payment. Now this is an OK work around unless someone used a credit card then you have a problem because now you are refunding the whole order so you will need to ring up a new purchase and customer needs to trust you that they will get original order fully credited. But until they fix, and they are saying they are working on it, you either do this or accept that you will never have proper reporting (or as I have said, you will be have fraudulent reporting).