If the initial programme was supplied and referred to in the contract data part two under the heading ‘The programme identified in the contract data is…’, then you cannot apply the 25% retention. This is because clause 50.3 makes it clear that it only applies if no programme is identified in the contract data.
there was a programme issued with the tender that was not referred to in the contract data, and
the programme you now have is the first one issued for acceptance since the contract came into existence, and
the programme does not show all of the matters listed in clause 31.2,
then you can apply the 25% retention.
There are though, two other things you need to be aware of. Firstly, this retention does not depend upon the project manager accepting the programme. As long as it has been issued and shows all the information it should, then the retention is not taken even if the project manager thinks it is wrong for some other reason. And secondly this is only a retention, not a deduction, and eventually it will have to be paid back.