Categories can be deleted in the properties dialog of the project.
They will be removed from the properties dialog of the applicable Cockpit
objects.
Select the category that you want to delete from the table of all defined
categories and use the button 
If the category that you want to delete is still used by one or more objects, you will get a notice and the deletion will be abborted. In this case assign a different category to all objects that still use the category you want to delete and then delete the category again.