I've seen this type of questions before but never seen a clear answer. What I did in one of my sites is change the CMS (to Drupal), so basically many of the content page URLs changed. I took it all under consideration and indeed many of the now gone pages where deindexed. It's been months now and it seems that Google does not index all the new page URLs, so basically I'm left with only the home indexed. I wouldn't worry about it unless it was going on for so long. It's been more than 6 months now and it simply doesn't make sense anymore. Any ideas?
I'm not familiar with Drupal but are the URLs friendly? I cannot remeber how drupal does it. If there is an SEO mod, install it now. How's your navigation? My CMS has a javascript navigation which isn't a good thing so you need to make sure the search engines can read your internal links, with a static navigation if possible. Next, have you submitted a sitemap? It helps google find all your inner pages
All the URLs are search friendly. Navigation is all direct links. Shouldn't be any problem with reading internal links. I've checked any problem with robots.txt and whatnot, everything is set right. It's not my first, second or third site.... This is just bizarre.