We are an eCommerce site with about 50,000 pages. We decided to focus on about 2,000 so google will crawl our site better. We planning to remove 48,000 pages from the sitemaps and from the site links, so it won't be accessible through the site. The pages will still be accessible if going them directly. Our concern is that these 'orphan pages' will damage our SEO. Are that many 'orphan pages' can harm our site? Redirection is not an option since we will use some of the pages in the future.
We are an eCommerce site with about 50,000 pages.
For an eCommerce website this is normal, as per sitmap.org, a sitemap can have 50,000 URL and size upto 50MB.
Therefore it's suggested to use indexed sitemap, which enable you to use 50,000 sitemaps, which is equal to [50,000 x 50,000 = 2,50,00,00,000 URLs].
Q: How big can my Sitemap be?
Sitemaps should be no larger than 50MB (52,428,800 bytes) and can contain a maximum of 50,000 URLs. These limits help to ensure that your web server does not get bogged down serving very large files. This means that if your site contains more than 50,000 URLs or your Sitemap is bigger than 50MB, you must create multiple Sitemap files and use a Sitemap index file. You should use a Sitemap index file even if you have a small site but plan on growing beyond 50,000 URLs or a file size of 50MB. A Sitemap index file can include up to 50,000 Sitemaps and must not exceed 50MB (52,428,800 bytes). You can also use gzip to compress your Sitemaps.
Q: My site has tens of millions of URLs; can I somehow submit only those that have changed recently?
You can list the URLs that change frequently in a small number of Sitemaps and then use the lastmod tag in your Sitemap index file to identify those Sitemap files. Search engines can then incrementally crawl only the changed Sitemaps.
I'll recommend you to go with indexed sitemap instead removing pages, from sitemap.
Removing page from sitemap will not hurt your SEO anyway and it's not the right solution, Google will crawl these pages as they exist.