NEC 3 Option B - Reduced Quants Extended Programme

I have an NEC 3 (Option B) which due to an error in the Employers BofQ will see final quantities significantly reduced. Running alongside this we have not achieved our tender outputs and as such the planned completion date is very similar/later then the original Completion date, despite the large reduction in quants. If we were to value this as a CE, calculating the difference between the forecast Defined Costs of the larger and smaller quantities, would we be entitled to include the cost of the prolonged duration, even though it is mostly of our own making, or should the CE be calculated on the basis that the work was completed in line with the contract programme. Is the Employer entitled to a saving in prelims due to the reduced quantities despite the contract duration being the same if not longer?