NEC Option E Defined Cost

An Option E contract included an agreed schedule of rates for the core works but unquantified. The schedule was bound into CDPt2 with reference to their use as Defined Cost. Subsequently cahnges to the works information included the agreement of new rates to cover these works. All rates have been used to assess the defined cost of these works and have been certified and paid as such. Is this allowed under an Option B, and can the PM at Final Account stage subseqenlty challenge the use of these rates as defined cost?