I recently completely redid one of my sites. The only file that was in the same place with the same name was my home page, index.php. I lost all
PR on every other page, but I imagine it will come back before long.
It has been about a month and most of my new pages are in Google's index now and most of the old ones are starting to disappear.
The key is to make a good custom 404 page. This will allow spiders that go to your site expecting to find a page to find
something to work with. On your 404 have links to the most important parts of your site and a sitemap which represents your new structure.
This 404 page will also help visitors who find you in the SERPS to land on a page of your site instead of the default 404 page. Tell them you redesigned your site. Give them a search function to help them find the content they were looking for.
I also set up a sub-domain and moved my old site there. On my 404 page I tell visitors that what they are looking for might be on the old site and I give them a link.
You can see what I mean at
http://www.divergentlines.com/error_404.php
There are tutorials all over the internet about how to do this with both Apache and IIS. Just look at a few and decide which method you want to use.
Good luck.