If during remeasurement of the Bill of Quantities on completion of works it becomes apparent that there are elements of work which do not appear in the Works Information and have thus not been completed, nor are they required by the Employer - how is this dealt with? If you apply Cl 60.4 the Contractor would be entitled to raise a CE but regardless of what he changes the price per unit to, as the quantity is 0, the price will be £0.00. Can they reclaim anything on these elements or are the Prices reduced?
Given the scenario - or real life situation - that you have painted, I do not believe that clause 60.4 is the clause that yopu should be looking at as all three bullet points have to be satisfied for it to be a compensation event. Clearly, the last one - rate x FINAL quantity > 0.5% of the Prices at the Contract Date - cannot be true if no work to which that rate was applicable was done.
Instead, I think you should be looking at clause 60.6 where there is a "mistake in the Bill of Quantities which "… is “due to ambiguites or inconsistencies”. I.e. an inconsistency between the BoQ and the Works Information is the compensation event.
60.7 states how inconsistency between the BoQ and another document is assessed with the Contractor “assumed to have taken the BoQ as correct”. In simple terms, for me, that means in building up your total Prices, you assumed that you would do that quantity of work and as result you are under recovering.