I think firstly, although you state that each Project is a compensation event, they are still just a part of the overall scheme of works under the main contract and as such can't be treated any differently, although there may be discrete reporting requirements in terms of cost, budget and progress etc.
You correctly notified an early warning relating to the delay to the critical start date. You don't state what 'follow up' actions were taken, although when the matter started to impact upon delivering the works then a compensation event should have been notified. You don't state what the cause of the delay was, but I am assuming that it was for reasons beyond your control, hence the Subcontractor holding 'plant' (NEC Equipment).
The Project Manager then instructed a PMI removing this part of the works. This is a further compensation event, presumably under clause 60.1 (1).
I am not sure what the status of the initial compensation event is with regard to the quotation etc, but the subsequent compensation event (PMI) would allow you to include any such 'abortive' costs within a quotation, where they are incurred as Defined Cost. As it was incurred via a Subcontractor, then they also don't need to be incurred in the Working Areas for it to be treated as a Defined Cost.
Technically speaking, ANY compensation event under Main Option C could incur an element of Defined Cost, even if it was simply for the preparation of a quotation, where applicable, and no actual works were undertaken.
I would advise preparing and submitting a quotation, consequent to the PMI, and include costs which you believe are appropriate. This allows the quotation procedure to be followed. It is possible that the Project Manager may make his own assessment under clause 64, but you have the right to refer the matter to dispute resolution where you formally disagree for valid reasons.