If you're reading this the DNS has successfully propagated.
At the same time as updating the site I took the opportunity to upgrade to WordPress 2.1. Aside from needing to change the blogroll categories and update the function in the template all went fairly well.
The blogroll has been merged with the other categories so if you were referencing your blogrolls and link list via id it's likely that your ids will have changed. The easiest way to find out what's going on is to go and look at the blogroll maintainence screens and look at the category links have changed to.
The other issue for me is that the wp_get_links function seems to have changed causing the links to be output with a load of brs etc. To fix this I looked at the code and found that the function get_links() did what I wanted. Thus I changed from this:
<?php wp_get_links(4); ?>
<?php get_links(37,'<li>','</li>','',false,'name',false,false); ?>
The difference being I am now specifying the markup before and after the links and whether to display the descriptions or not.