From the shop page: https://tests.demo.superspeedyplugins.com/shop/ each size has 2 products in the product count on the filter.
Large: https://tests.demo.superspeedyplugins.com/shop/?filter_size=25
Medium: https://tests.demo.superspeedyplugins.com/shop/?filter_size=26
Small: https://tests.demo.superspeedyplugins.com/shop/?filter_size=27
Set both sizes in one variable product to out of stock and that product no longer appears in the sidebar product counts, or on the page.