Should the weight of the lifting surfaces be deducted from the weight used to calculate the C of G of the aircraft? If the aerofoils are creating lift they are doing the work to lift the helicopter.  When the helicopter is hovering, the blades are carrying the weight of the entire ship. The forces on the aerofoils are acting in the opposite direction to gravity which is pulling the ship down. These opposing forces create a situation where the ship is now hanging from the aerofoils. 

So would this mean that the weight and balance calculation for the pilot should not include the weight of the aerofoils as this weight difference would affect the C of G? 

A fixed wing aircraft would suffer the same results?

My question is, should the weight of the section of the aerofoils of an aircraft  that provide lift be deducted from the weight used to calculate the C of G of the aircraft?
The center of gravity is relevant for all inertial forces. For example, if you turn, the centrifugal force would be calculated with the mass of all aircraft parts, including wings and rotor blades.

If you want to calculate the loads on the aircraft structure, things depend on the location. If, for example, you want to know the load on the wing root or the helicopter rotor shaft, you use the total mass minus wing / rotor mass times the acceleration to calculate the force.

While there are cases where the wing mass needs to be subtracted, center of gravity calculations must include it.