I also posted this same question to support.puppetlabs.com (issue arose while working for an employers with a PE support contract). The response I got back through that channel informs me that a feature request for an 'unset' target to the puppet config command has been created; and that in the mean time:
However to answer the question "If we set the new server address in both the main and the agent sections, will the duplicate create issues for us?" it depends. If they are not the same certname than yes agent runs will fail. If the server setting is just a duplicate and has the same certname than it will not be an issue.