Microsoft Knowledge Base Article 889250 contains the following summary:
When you uninstall a certification authority (CA), the certificates that were issued by the CA are typically still outstanding. If the outstanding certificates are processed by the various Public Key Infrastructure client computers, validation will fail, and those certificates will not be used.
This article describes how to revoke outstanding certificates and how to complete various other tasks that are required to successfully uninstall a CA. Additionally, this article describes several utilities that you can use to help you remove CA objects from your domain.