Questions
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Will updating our site from ASP .NET 3.5 to ASP .NET 4.0 negatively affect SEO?
If your ASP code is used primarily for dynamically generating HTML (at or before page load), and the HTML isn't changing, and your URLs are staying the same, I can't see how SEO would be affected or why you'd run into any problems. If the upgrade includes code modifications that change the way the pages load, however, it could affect SEO depending on how that's handled.
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