When you copy the gradebook from an old course site to a new course site all of the items come across and are available to your students. They are also included in the course grade calculations. This can be confusing to both you and your students. 

There is not an option to bulk edit the items in your gradebook and make all of them unavailable to your students and not included in your gradebook calculations. That way you can turn them on when they have been graded. 

The video (1:52) below demonstrates how to bulk edit the items in your gradebook.