I face the following problem: I have a site based on Wordpress, the site is built with several plugins using many resources (do a lot of queries). I want to make a homescript much better? In the script version that will make the current data and index pages (25,000) will be lost (no data have great importance in this time). How can may not be penalized as long as I appear in webmaster tools page not found?
If it makes 25000 url lost then it will create so many 404 error and surely it will not be good for you site. To avoid this you can block such url or directory via robots.txt or 301 redirect all 404 pages to your home pages.. Once I found such discussion in same DP forum on how to redirect all 404 pages in wordpress. It was very useful for me. You can try it too before making such changes.
Google doesn't like pages that are showing the page not found errors. The sites that have a large number of such pages are eventually punished or penalized. Make sure that the sites do not have such pages.