Hi, Leonidas,
I’ve just replied in the wp.org forum thread, but just in case, I’m posting the same here:
I think that the “Filter Everything” plugin is taking sale prices directly from DB, i.e., from product meta, and our plugin is using filters to apply discounts, e.g., woocommerce_product_get_price
.
The only solution I can see is to create a tool that would go through all products in your shop, apply our plugin’s price filters, and save each product’s new sale price in DB. I believe this would solve the issue with the “Filter Everything” plugin, however, you would need to use our plugin a bit differently, e.g., each time you change the discount percentage, you would need to run the tool again, so it would go through all products and assign new prices (now the plugin is applying new prices immediately, without the need to run any tools).
Please let me know what you think.