Khan2Canvas can work with cross listed courses where multiple sections have been combined on Canvas 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 cross listed together on Canvas 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.
When creating assignments on Canvas that are to be used in Khan2Canvas, they must be assigned to all sections. Khan2Canvas will produce an error if you try to send scores for an assignment that is not assigned to all students.