Designing a new website, or redesigning an existing one often necessitates some restructuring. Information Architecture or “IA” is an interplay between a. the data model / database schema / content types, b. The navigation available to users, and c. the URL structure. Design of the URL structure should be informed by SEO, design of the navigation should be informed by UX, and design of the data model should be informed by product design. It’s more of an art than a science, and the overall goal is to make it easy for users to find what they’re looking for.
An important consideration in terms of SEO when restructuring an existing website, is that most or all of the URLs on the old site should 301 redirect to new URLs. A lot of the time we can use bulk redirects to handle content that is following a redirect pattern, but in general it is always wise to maintain an inventory of all of a website’s URLs, and to test all of the old URLs to make sure that they’re forwarding as-expected prior to launch of the new site. Launching a redesigned website with a lot of broken URLs is a major SEO faux-pax, and could result in a loss of pagerank.