I had our tech dept put in the noindex/nofollow about 5 days ago, and now there are no pages listed on Google. I figured this was a necessity in order to avoid all the SE friendly URLS of the pages already indexed sent to the duplicate content chasm. Is this a common practice when you're switching to SE friendly urls?
Umm, you should 301 redirect old URLs to the new URLs.... not nofollow\noindex them. You will lose all Pagerank value and SERPs doing this. 301 redirect all old URLs to the new ones ASAP.
The old urls will still exist, but we want the SE friendly ones to be in the search engines instead of being considered duplicate content.
Why? If you 301 redirect them it's the same thing; minus the extra web pages. This is the proper way to do it.