A bit confused about sitemap.xml . Google search is listing completely wrong information and dead links. I've submitted a sitemap to google and waiting for updates, but when I looked into the generated file, it is including all the collections from the site including outdated and hidden ones. How can I make the sitemap reflect my navigation menu?
What do you mean by outdated and hidden? Just because a collection is not accessible on the front-end, doesn't mean Shopify knows to exclude it from the sitemap.
If you have a collection you don't want showing in SERPs, either delete it from Shopify or set a metafield value of 1 for the namespace seo. Search "metafield" in my Shopify SEO guide for more information. Using that method with metafields, you will exclude a published collection from the sitemap.