Khan2GC can work with cross listed courses where multiple sections have been combined (cross-listed) on Google Classroom but still have separate classes on Khan Academy.
To include a cross listed course, select the primary course as usual when going through the setup or when choosing a course using the Settings sheet.
When importing data is important that you always include reports from all of the cross listed Khan Academy classes. If you have 4 Khan Academy classes combined together on Google Classroom and only include a report from one of them when importing data, scores will only be available for students from the one Khan Academy class. The scores of students in the other classes will show as missing.