I am not sure what the programme being reference to an early warning here means. There is no such thing as EOT under this contract, but if a compensation event has delayed planned Completion then you are able to assess the impact of that within the quote and move the Completion Date by the same amount. To assess any compensation event you use the last Accepted Programme, which is the original one unless another has since been accepted. however, I believe you should take into account progress and other things that have happened prior to the compensation event becoming apparent (although the contract could/should be clearer on this point.
Without at all wishing to sound rude, I am afraid your question appears to demonstrate a general lack of understanding the contract as a whole(which is indeed what we try to help with in this portal). Why are you notifying programmes under an early warning? Why are you talking about EOT rather than a delay to the Completion date? Why has there been an apparent lack of regular submitted programmes and subsequent acceptances? Why did your latest programme not show all of the works that needed to be done??
Sorry if this does not seem very helpful but I have more questions about your “question” in order to begin to be able to answer it/them.