Steps to reproduce:

• Create a test course with two or more sections using the topics format.
• Create an activity in each topic.
• Hide one of the topics.
• Create a CSV file with shortname, fullname, category, format and templatecourse fields. Set the templatecourse value to the shortname of the test course, format to topics and everything else to some suitable value.
• Import that CSV file using the "Courses > Upload Courses" function.
• Go to the newly created course.
• The topic that was hidden in the original template course will now be visible, although the activities it contains will still be hidden.

The root cause of this problem seems to be a minor bug in backup/moodle/restore_stepslib.php, so I've tagged this as a backup problem. It might affect earlier versions of Moodle, but this is the one where a customer reported it to me. The attached patch fixed this for me, but I can't say if it has other knock on implications.