Here are things that I believe to be true about Huge Ships and Conner Nets.
If a Huge Ship hits a Conner Net both of its sections lose their actions since the ship loses its Perform Action step.
If a Huge Ship hits a Conner Net the tokens would reduce the amount of energy that is generate by the maneuver that is being performed.
I'm not too sure about the damage. Does it get assigned to the section that hit the Conner Net or can it be allocated to either section?