one of my sites had a complete link structure changed, I get over 300 link error in google webmaster central, and this stayed for few weeks. When can I expect to get my pages re-indexed?
Yes you can. As I know first you have to request google to remove the links. You can use the google web master tools to do that. Then submit your new site map and social bookmark the site.
Even if you remove your old urls through google url removal tool, Google will still show those url as error for some days. It takes some days to update their error db for your site. Make sitemap (xml and html) for your site with the new urls and submit it in Google. If some of your old urls have some PR, don't afford to loose it. Try to setup a 301 redirection to new url.