This is a bit of a placeholder article for now to bring together useful links about how to update content types and lists defined in a feature. Modifications to list instances—and propagating those changes to content created on the original instance—are notoriously difficult but it seems like it can be done.
http://stsadm.blogspot.com/2008/05/propagate-content-type-changes.html
http://soerennielsen.wordpress.com/2007/09/11/propagate-site-content-types-to-list-content-types/
