The Free plan puts every active product in the file, even if the store has more.
The other products stay in Shopify and in the sitemap. They are not deleted. They are simply outside this short index.
The cap
- every active product at most
- Pages, policies and collections are separate from that cap
- Uncheck products if you do not want any
- The sitemap remains the full URL list
Choose the products that matter by how Shopify returns them for the task, and use collections when a category link is more useful than 25 individual products.