Could be, last saturday (7 days ago) I completely changed a PR5 site, had to, it was a mix of php and html and folders and files all over the shop, it grew out of control in other words. Relatively small in size 80 odd pages.
This is the process I took (after reading here of course) I knew it was bad move but neccessary.
Completely built new site on spare domain first
Created 301 from old page to new pageORcategory for every single URL I couldnt do a mod_rewrite as it would have taken ME longer than the 301's
While creating the htaccess file I did the non www to www, index.php to / and the 404 just incase
Last Saturday morning, did a final check, deleted whole old site and uploaded new version with .htaccess, re-created G sitemap and told them to fetch it again.
This morning checked G sitemaps for errors, had 1, they wanted the site verifying again (could be coincidence as a few other sitemap sites have asked in the past for re verifying) chose meta verifying version, uploaded index.php verifyed OK, ran site: from within sitemaps and ALL new pages are indexed, and a few suplimentals, traffic over the week has been higher than average, added the sup URL's to the htaccess.