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My site just under went a huge modification in terms of beautification (new format, template, css, rss, etc.) The navigational structure also changed.
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I am going to assume you didnt change any of the urls for your existing pages.
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I regularly submit the google sitemap. Isn't that the same thing as you mention submiting to google
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Yes if you submit to sitemaps then it will help google index those pages. I am sorry but I dont remember your site. Is it a advanced access site? I do not use google sitemap but its my understanding that you have to give each page a rank so to speak of its importance. If this is so maybe you havent given those other pages enough weight in sitemap to tell google they are important.
Do you also have a sitemap on your site? If so do you link to your sitemap from your homepage?
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I take a closer look, the pages that google is showing with the site: command are only those that are linked from my homepage. This is a small % of my pages. I have many pages off pages, etc.
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it could be a number of things. Maybe unfriendly urls, no links pointing to those pages from an already indexed page. I would suggest maybe creating a sitemap and placing that link on your homepage and also listing the sitemap in a directory to maybe get google to visit that page from the directory and hopefully getting them to visit each of those pages to index.
There is some problem however. Whether it be google just hasnt found them because of site structure or something else. I would maybe also suggest looking at your site structure to see how it navigates to those pages that are not indexed.