Hello,
Custom layouts override the default WooCommerce pages on the frontend, but the original WooCommerce pages will still remain in the WordPress dashboard and are not removed automatically.
If the custom layout is not taking effect, please make sure that the layout is Active and that the correct Conditions are assigned to it.
If the issue remains, Kindly share the page URLs that are still showing the old design along with screenshots of the layout conditions, so we can investigate this further and help you determine why the layout is not being applied.
Further, you can read more about the Layout Builder here: https://xtemos.com/docs-topic/woodmart-woocommerce-layout-builder/
Best Regards