You can remove specific instances and pins from the active cone. You cannot remove nets and ports from a Logical Cone.
To remove only selected objects from a cone:
Make sure the cone you want to remove objects from is the active cone.
Select the object(s) you want to remove from the cone.
From the LogicalCone menu, choose Remove From Active Cone>Remove Selection.
The selected objects no longer appear in the active cone. If some of the selected objects are pins, their corresponding instances are removed as well.