Okay so looks like now you are only having the order management addon related issues. Both the following issues will be taken care of in the order management plugin soon:
– WP eStore Order management is not showing the correct status – they all show as ‘complete’
– When you issue a refund from PayPal, the order management addon will update the order status to say “refunded”
No, it does not generate any email for affiliate commission reversal. It is not a standard practice.