It is not clear from your question what event the CE was notified for, a pricing error by the Contractor is not a reason for a CE.
If there is a rate in the BoQ for acceptable then this is the rate that should be used but mindful of clause 60.4 that provides for a CE (revised rate) if the final quantity of work (disposal of acceptable) meets the criteria set out in the clause. Also clause 60.5 which provides for a CE if the additional quantity causes a delay to Completion, which if it is the same overall quantity would appear unlikely.
If there is a rate in the BoQ for acceptable then this is the rate that should be used but mindful of clause 60.4 that provides for a CE (revised rate) if the final quantity of work (disposal of acceptable) meets the criteria set out in the clause. Also clause 60.5 which provides for a CE if the additional quantity causes a delay to Completion, which if it is the same overall quantity would appear unlikely.