It's not clear from your question if the Contractor is late due to issues of his own making, or if it's the restrictions on the project that caused it? If those restrictions aren't his fault then they may be entitled to compensation events that would move the Completion Date and / the sectional Completion Date.
The programme shouldn't have been accepted if it didn't show a realistic date for planned Completion, however the fact that it was doesn't affect the Completion Date or sectional Completion Date. It may skew how compensation events are assessed though.
The PM should only certify sectional Completion and Completion when the test at clause 11.2(2) is passed, there's no concept of partial sectional Completion, it doesn't exist within the ECC. Also there would be no compensation event for the Contractor failing to complete their works. Any compensation event would have to be for one of the events listed under clause 60.1 and also not to have arisen due to the Contractor's fault. Which takes us back to what was the root cause of them being late?
I've no idea why you would mutually agree that something happened when it didn't, also unless the PM certifies sectional Completion and Completion in accordance with the contract i.e. formally in writing, then it hasn't happened. It's possible that if there is a minute of a meeting recording that the PM has agreed to certify Completion on x date, that this may be enough evidence claim that it has occurred. However you'd need to look closely at the words and ensure the minutes are agreed as factually correct to establish this.
Clause 30.2 is referring to sectional Completion and Completion of the whole of the works, 30.3 refers to Key Dates and does not require the PM to certify this.
Without knowing more about the project it's difficult to comment further on what the Contractor may or may not be entitled to, and what the PM should / should not have done. What I will say that it sounds very strange for a contractor to settle for time with no cost, I suspect they realise they are culpable for some / all of the delay. You really need to get to the bottom of the root causes of delays before you can establish liability and entitlement.
The programme shouldn't have been accepted if it didn't show a realistic date for planned Completion, however the fact that it was doesn't affect the Completion Date or sectional Completion Date. It may skew how compensation events are assessed though.
The PM should only certify sectional Completion and Completion when the test at clause 11.2(2) is passed, there's no concept of partial sectional Completion, it doesn't exist within the ECC. Also there would be no compensation event for the Contractor failing to complete their works. Any compensation event would have to be for one of the events listed under clause 60.1 and also not to have arisen due to the Contractor's fault. Which takes us back to what was the root cause of them being late?
I've no idea why you would mutually agree that something happened when it didn't, also unless the PM certifies sectional Completion and Completion in accordance with the contract i.e. formally in writing, then it hasn't happened. It's possible that if there is a minute of a meeting recording that the PM has agreed to certify Completion on x date, that this may be enough evidence claim that it has occurred. However you'd need to look closely at the words and ensure the minutes are agreed as factually correct to establish this.
Clause 30.2 is referring to sectional Completion and Completion of the whole of the works, 30.3 refers to Key Dates and does not require the PM to certify this.
Without knowing more about the project it's difficult to comment further on what the Contractor may or may not be entitled to, and what the PM should / should not have done. What I will say that it sounds very strange for a contractor to settle for time with no cost, I suspect they realise they are culpable for some / all of the delay. You really need to get to the bottom of the root causes of delays before you can establish liability and entitlement.