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Is there any way of getting Yahoo directory entries updated other than submitting the site to the correct category? (Which I've tried once without any success.)
Setup a 301 redirect from all instances of one version to the other. We normally go with the www versions, so all pages on the site that start with [domain.com...] will have a 301 to their [domain.com...] equivalent.
Yahoo's customer service is spotty. You can try to contact their support team and have the directory listing updated.