brinked - 5:56 pm on Nov 4, 2012 (gmt 0)

Nobody here can really give you the answer you're looking for. There are just too many variables in play.

When you change your site structure you are usually changing a lot of different things on your site. Your site will need to be thoroughly reviewed.

There is some correlation between panda and site navigation, and a poor navigation can cause a panda penalty.

I had a client a few months ago who was in a similar situation as yours, it turned out he enabled rel canonical on some pages, but it in fact was canonicaling all pages to one page on the site, causing a massive site de-index. Such a simple thing was overlooked for many months.