The same exact thing happened to me. I inquired on IRC and Joel Aufrecht was kind enough to give me a few pointers that got me going in the right direction. Based on what I've learned (and hopefully others will correct me if I'm wrong), you're best option is to do a merge after importing the new sources: do a checkout using the double j syntax, the first -j being before the import and the second -j being after. That will give you a checkout with the obsoleted files marked for removal. Commit from the root of that checkout and the obsoleted files will be removed. I found tagging the tree before and after the import helpful. Andrew Grumet wrote up some CVS documentation that might be of further help. It's called "Advanced CVS for .LRN Development" and is under the dotlrn project documentation on openacs.org.
