Hi Miguel

Are you using the course score field in the program to calculate the minimum score to determine the course set completion criteria?

I don't see how making a course not visible would affect the calculation. The not visible course would not be able to be enrolled in but those who have already enrolled in the course would see this and course score field  counted.

Enabling audience visibility does mean that the viewhiddencourses doesn't apply but it is still able to set the audience visibility to No users if required. 

The course completion editor does have a bulk fix problems  for some types of problems identified otherwise records need individual editing as activity completion uploads are not possible . It is only possible to upload course completion records.

regards