The PM has to certify Completions under clause 30.2 and take over under clause 35.3. It therefore appears that the Project Manager is in breach of these two obligations x 3 times. Neither of these are compensation events and if they were, you would ten have to establish the effect on your Defined Cost.
However, under 35.2, the Employer takes over a part of the works when he begins to use it, except for a reason stated in the Works Information or to suit the Contractor's method of working.
Under X7.3, any delay damages are reduced from the date that the Employer takes over by the amount of benefit that the Employer receives as a proportion of the benefit. I.e. if the Employer is getting full benefit as if he had completely taken it over, the damages are zero.
So the answer, from what you say, appears to be 'Yes, he can change damages, but only for the remainder of the works, not the structural foundations'.