Well they have taken the decision to go to court so they are likely to ignore any correspondence at this stage.
I think you have two options, pay what you think is due with a strong letter saying that you will defend any action for the balance, look for your costs etc. Pay in the form of a cheque and say that it is offered in full settlement. If they cash the cheque you have an argument that they accepted that as full settlement.
Or pay nothing, on the basis that they are trying to overcharge you and put up your defence in court.
While generally paying something to people who take you to court only encourages them, in this case perhaps if part of what they have sought is due perhaps you should pay as much as you think is due.