You can use Google Webmaster tools to flag up pages that should be de-indexed once they have been 301'd or if they now 404. This should speed up the process and ensure that pages that don't get indexed very often don't hang around.
Best posts made by MulberrySqCraig
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RE: What is the most effective way to migrate an ecommerce site?
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RE: Sudden drop in rankings
Thanks, I'm pretty pleased with the site and the client is certainly happy with their sales so far!
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RE: .htaccess when integrating one website into another
You should be able to achieve what you want by redirecting 404s. You can do this by adding the following to your .htaccess
ErrorDocument 404 /homepage.html
Where homepage.html is the address of your homepage.
What would be better really though is to land them on a an actual 404 page that explains that the page doesn't exist anymore and gives them options of where to go next. Include direct links to the most popular content on the site.