Using GraphQL to update your Shopify store should not directly affect the inclusion of products in the sitemap. The sitemap is usually generated based on the settings and configuration of your store, rather than the specific method used to update it.
Search engines may take some time to index and include new content in their search results and sitemaps. It’s possible that the search engine hasn’t yet crawled and indexed your new products. Give it some time, and they should eventually be included!