Here's another example of how pages got stuck in supplemental. I decided to change the extension to .php from .html and all the pages that we're .php became supplemental. Google thought that they were identicle to the .html that no longer existed so they put them into the supplemental results. I guess I can only hope that Google comes through and sees that the .html pages don't exist anymore and takes the .php pages out of supplemental results. Lesson to be learned: If your going to change your extensions make sure that you change the content as well so they don't get put into supplemental as duplicate pages. Hope this helps everyone
This might be of some help. You can remove certain pages from googles index http://www.google.com/support/webmasters/bin/answer.py?answer=35303
yes, that is an idea but do you keep the old .html pages active? then you have duplicate content with a 301 redirect. Eventually the .html pages should be deleted so when do you do it? I figured just get rid of the .html as soon as possible with the .php pages. the .html would be noticed as missing and the .php would be the new replacements. I will try this here and see if it works. User-agent: Googlebot Disallow: /*.html$
Regardless of whether you've deleted or kept the old pages you need a 301 redirect to tell Google that the extension has permanently moved from .html to .php that's the easiest & most effective solution.