Tar the course (tar -czvf <name_of_tar>.tar.gz dir_to_tar/)
Re-import the course
Voilà, the second problem is no longer in the course tree, but hasn't been removed from the course.
To verify, in studio, go to /orphan/<course_id>
Note: exporting a course walks the course tree, so if you export a course with orphans, and import it into a new course, that new course won't have any orphans. If you want to play around with a course that currently has orphans in a safe way, you should rerun the course–that does preserve orphans.
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