No, most of your permalinks are dynamic, so they will change along with the overall permalink change. The only permalinks that won’t change are ones that have hard-coded <a href=""></a> tags. For example, if you have linked to post B inside post A, then you will have to go back and change post B’s link inside post A. Your Google pagerank may also be affected, as the bot’s index of your site may have to “rebuild” because of the new link structure. To avoid that, use a Google Sitemap. See: http://codex.wordpress.org/Search_Engine_Optimization_for_Wordpress#Google_Sitemaps
Yes, it will (that is in regards to older permalink links). However, if you prepare a bit in advance of the change, you can avoid breaking old links (if using .htaccess and mod_rewrite). All it takes is to copy your older rewrite rules from .htaccess, and after updating the permalink structure paste them back in (under the new ones).
Question: If I use this method (copying my old .htaccess rules into my new .htaccess to keep my old permalinks working), do I need to add the R flag to them all to make them 301 redirect?
