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I have personally done this in the past, it didn't affect at all my rankings and it could even be seen as a benefit for your users. I guess you are going with an Apache web server, make sure to set 301 redirects from the .php versions to the [no extension] URL (via the .htaccess). Even if the user types index.php, you should create a rewrite rule to remove that .php and set a 301 in the process. Hope that helps!

When we moved our site over to full HTTPS we noticed that GWMT needed to re-authenticate for the HTTPS domain, and actually shows different information from the HTTPS profile compared to the HTTP profile. The Analytics proporty won't change, but your sitemap will need an update for provide the HTTPS links compared to the HTTP ones. Google will quickly pick-up the protocol change and as long as you set-up correct redirects from HTTP to HTTPS you won't be dropping traffic that much. In the long run you'll see your site returning to it's old self again, depending on how good the rest of your optimization is. Do keep in mind that if you're mixing content (retrieving external content from HTTP sources) some browsers start throwing warnings to users; if you're embedding HTTP content in an HTTPS site, browsers like Chrome don't load the HTTP at all unless the user clicks the option for mixed content at the end of the address bar. Hope this helps!

Hi! When you choose your preferred domain between www and non-www, you must declare ownership of both. So don't delete any domain from your account. This is most likely the reason you have both domains on your GWT. Here you can see the GWT Help and verify what I said: "You may need to verify ownership of both the www and non-www versions of your domain. Because setting a preferred domain impacts both crawling and indexing, we need to ensure that you own both versions" Cheers.