I have removed the "clear" link from the theme's php file so that the clear option does not show up when a product variant is selected. The link is now gone, which was part of the goal, but the Clear link still has an effect on the Add to Cart button, moving it down about 30 pixels once a product variation is selected. I'm using the variations sample of the WooCommerce plugin to implement a button look for product variations. When not using the variant samples plugin, clear links appear to the right of the list, but when using the plugin, the links appear below. Wish I could insert an image here. Any help will be greatly appreciated. Thanks!
add_filter( 'woocommerce_reset_variations_link', '__return_empty_string', 9999 );
Don’t the prices that appear after selecting a variant move the button down?
Otherwise something to consider might be; the element that is the parent container of the transparent link still appears in the html, and the filter you add just replaces the inner html with an empty string. Since the parent container still exists, it still takes up space on the page and may move other elements down. View the rendered html when testing selected variations. Use Chrome Dev Tools to view the html while testing.