Right. Sorry this took time to get under my radar. So, I went thru the code to get familiar with this area. Big thanks to Dan for all his awesome work on this. His code is clean and easy to follow.
So, I have executed the script to populate the PHM cohort at the clone machine. It put total of 107 users into it. There is one thing that will not make Helen happy though. We can't use that cohort manually pre-created. As we are going to use this externally maintained cohort, it can't be created manually. The script created a new cohort "Particularly helpful moodlers" (note the lowercase m). So all the cohort-to-group-members enrolment plugins in all courses have to be updated to use this new cohort instead of the manually created "Particularly helpful Moodlers" (note the uppercase M):
I have tested the enrolment plugin in the Czech community course and it put just myself into the group:
More testing is required I would say. Also, IIRC the cronjob is not running at the clone which may or may not be related.