Generally, if you make good changes, you'll see a short-term dip before a long-term increase. The challenge is differentiating between bad changes that have caused long-term harm, vs. good changes that are experiencing the natural short-term dip.<p>A website may build good reputation with a search engine which has ranking benefits but at the core of search engine ranking is individual pages: you must protect your well ranking pages at all costs. That means <i>never break any links</i>. If you break links, your pages will drop out of search engines, and it can take years to rebuild the lost reputation for those pages. The model for thinking about SEO should be page-based, not website-based.<p>The good news is that if your website was able to rank well once, it'll rank well again, because as much as we might tinker with the structure of a website, what matters most is the content, and you're still distributing that same content... you just might have set yourself back a year by breaking a bunch of links. Easy mistake, c'est la vie.<p>The ideal strategy for experimenting with SEO is to do it page by page, experiment with different changes on different pages and measure the impact. Don't make wholesale changes to the structure of every page until you're confident that you're doing something that works.