As you know GitHub has introduced a Repo Transfer feature. https://github.com/blog/876-repo-transfers
This allows you to change ownership of your root repos, not forking them with your organization. However, if you have already forked a repo and want to dump all its open issues to newly created one, what should you do?
Is there any solution on GitHub-2-GitHub issues import?
Though Tekkub answer makes sense, I still implemented a short script to transfer issues:
github.com/…./gh-issues-import