1. Making major changes to a site often causes Google rankings and traffic to drop, at least for a few weeks.
2. A small loss of "pagerank juice" occurs when a 301 re-direct is used. This means that the entire site will be slightly weakened permanently.
3. There has been speculation that the Google algorithm gives less trust to sites that have large numbers re-directs, deleted pages, and other indications that a site has undergone a major structural revision at some point in the past. It could take years to rebuild any trust lost in this way.