Ok, so there seems to be a couple of related problems. 1) when changing the user permissions of a Blocks in a Course Site e.g. Removing Student, they aren't carried across on an individual Restore of the Site. 2) By changing the permissions of a Block in a Course Site, that site can no longer be used as a Template to Restore from using the Upload Courses process. The Upload Courses process fails.
(By the way, from a usability point of view, there really should be a visual means of Course Rollover (Automatically Backing up Courses, Restoring a historical course copy, and Resetting the current Course for new enrolments without the need for CSVs or Command Line. )