With Google's Webmaster Tools, they are only an indication, not an absolute. If you have changed the URL structure, did you put re-directs in place to tell google where to find the new content?
Have you checked wmt for errors relating to the sitemap?
I can match exactly what you say with one of my own sites, in that I've changed the design / layout and given a new Sitemap, it lists 6 out of 200 in the new sitemap, rather annoying.. but what can you do, Google knows best?!