Here is the problem when one Party or other is not following the contract. If you submitting a programme at tender stage and it was referenced in contract data part 2, then by default that is the first Accepted Programme. Subsequent programmes have to be accepted or not accepted by the Project Manager - there is no such thing as it being “deemed accepted” due to lack of response. The Contractor has to escalate this at the time and one way or another force/encourage the PM to respond with acceptance or rejection so both Parties know where they stand.
If i was your PM I would look back at those programmes and see if there would have been a reason to reject them. Either way you need to get back on track of which I would suggest a two phase approach:
- submit a revised programme showing where you are now and what works are left to do and hence where your planned Completion is.
- separate exercise to justify why planned Completion is beyond Completion Date (if indeed it is) and be able to justify which specific compensation events that was down to.