Hi I have the same problem, after update to version 2 , in the product category nothing is showing. In some cases where we have out of stock product in the category, it only shows the out of stock products in the categories. other product not showing up. It also has conflict with WordPress product filters widget when you applied specific filter from products attributes where you have defined on Woocommerce, it shows out of stock products. It seems it is related to existed conflict between your plugin and the queries and filters in Woocommerce. I did not put check mark to hide discontinued product.
The other problem is that it does not replace the price or out of stock text with discontinued text. in the product page and in the category page.