To deactivate competency you first need to access the Competency Link on the Left Navigation Bar. 
You will need to click on Administration and select the Competency. 

When you are on the Competency Page, you will need to select a department and course you want to deactivate a Competency. 

It will come up with a list of competencies which you can deactivate. You will need to click  green switch to deactivate the competency for the course.The switch will now appear grey indicating that the competency is now deactivated