Look at option B clause 60.6. It sounds as if the Project Manager is making corrections to the BoQ "which ... are due to ambiguities or inconsistencies." Note that the conditions do not say between what documents so it applies to the whole of the contract. I.e. the BoQ says one thing and the Works Information says another.
The last sentence of 60.6 says this can reduce the Prices and 60.7 gives additional (to that in the core clauses) direction on how it is assessed. You will therefore only need to agree the Defined Costs you are NOT incurring in doing the work described in the BoQ, NOT the cost of your prelims.