Choose which brands and categories each channel receives

Whether an empty brand or category reached a channel wasn't up to you. It's a setting now: open a connection's settings and, under Taxonomy, pick All categories, Only categories with products or No categories, and the same for brands. Only categories with products is the default, and a parent category counts if it or any subcategory has products. Choosing No categories removes what is already published, so the line under each dropdown says what will happen before you save. The other connection settings are in Settings.