With difficulty !
The first thing to say is that the financial assessment is not directly linked to having an Accepted Programme as it is not mentioned in the key clause of 63.1. So in assessing the financial aspects, you can make reference to the submitted programme and the impact etc on method, time scales, use of resources, time in the Working Areas, risk and cost (in approx. that order).
It does become more tricky with assessing the time and contractually changing the Completion Date as clause 63.3 does make direct reference to the Accepted Programme as the reference point for how change is evaluated. Here I hope some common sense prevails in that if, for instance, the PM has accepted the change in Defined Costs is partly made up of changed costs for prelims of, let's say a week, then he or she would be inconsistent in saying that the CE has not had that same affect wrt to the Completion Date.
But strictly b y the contract, that does not matter. Having said that, the latest case law on NEC seems to indicate that the courts don't care what the contract says ! See my comment here : https://www.linkedin.com/groups/2893228/2893228-6271255410993299458