It looks like you are referring to the NEC ECS (Contractor accepting CEs) but the comments apply to both the ECS and ECC forms.
Firstly as access is stated to be 'agreed later' then I can only assume that you would need to agree with the proposed second section access dates, rather than just accept what is offered to you.
You need to show contract access dates in your programme although you can show a later date if that is more appropriate or it changes due to circumstances, such as a delay to a previous section. This later access date is then used to assess a compensation event under clause 60.1 (2) for an Accepted Programme.
You don't say what caused the delay to the first section and whether it was a compensation event, although if the first access date for the second section was stated in your programme (as accepted) and it was not given then that is a compensation event.
In answer to your questions;
1. The programme does matter as you can put your own required access dates (later than the contract access dates) in an Accepted Programme which become the 'measure' for a compensation event, Any entitlement would, therefore, be based on the programme access dates. From what you have said it looks like the first access date for the second section is dependant upon completion of the first section works, If the delay (from week 25 to 28) was not a compensation event, then the Contractor could have stated that the CE arises from a fault of the Subcontractor, in not accepting the CE.
2. A CE notification should relate to an event, so each access date separately, where appropriate.
This is not an ideal situation with 'unknown' access dates but I appreciate that this does actually happen, giving rise to uncertainty and dispute, as is evident in your case.