I just found this issue when looking into Google webmaster tools to find out why my site is not showing up on the SERPs all of a sudden. I changed my permalink structure in Jan 2011 to include the %year% before the postname as my site would not load. I have a huge amount of pages and using only the %postname% permalink caused a time-out. As of right now, the upgrade to 3.1 has changed all permalinks to the present year (2011) so all posts prior to the start of 2011 are going to a 404 page. I don’t believe there’s any way to manually edit that part of the permalink either. I’ve tried to use permalinks migration to change to a post_id instead of the year but it resulted in all links being broken.
with all the broken back links my site is now in never-never land. Any thoughts?