Hi sohee7569,
Thanks for reaching to us.
1. When you make the product out of stock in the inventory tab it will be out of stock and it will not show in the frequently bought together.
2. I kindly recommend you to build Custom Single Product layout, which is built with WoodMart WooCommerce builder, then you can re-order product content positions without using Custom PHP code.
Further, you can read more about the Layout Builder here: https://xtemos.com/docs-topic/woodmart-woocommerce-layout-builder/
Regards,