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Install the Ad-hoc database queries (customsql) plugin.
Create a new Custom sections course.
Add a subsection.
Delete the subsection.
Remember the course ID.
Go to Site admin > Reports > Ad-hoc database queries
Add a new query:
SELECT * FROM {course_sections} WHERE course = [the course ID] ORDER BY section
(inserting the course ID as appropriate)
Verify the subsection isn't shown.