The main contractor has misunderstood the contract. The removal of these piles was a change to your subcontract works information and as such was a compensation event under clause 60.1(1). That change is not valued based upon the rates in the bill of quantities but by forecasting the effect it had upon your defined cost, and then adding your fee, see clause 63.1.
So, you forecast what the defined cost for the omitted works would have been and add your fee. You then deduct the bill of quantities value of the omitted work. If the difference is a positive figure, that is it would have cost you more than is in the bill of quantities, the total of the prices is reduced. If the difference is a negative figure, that is it would have cost you less than is in the bill of quantities, the total of the prices is increased.