On the "Grades" screen you can filter the students who appear on the screen so that it only shows active students or only shows a particular section of a merged class. However, the exported gradebook csv file shows everybody (active, inactice, all sections and so forth). The exported gradebook should recognize the filters used in the grade screen.
I noticed that parts of this have already been requested. For example. there has been requests that only active students are in the csv file or only individual sections should be exported. If the exported csv matches what is seen on the screen this will take care of all these issues.