Under a Main Option E, costs are either 'disallowed' because they do not comply with the category requirements in the Schedule of Cost Components, the definition of Defined Cost or they are a Disallowed Cost because they comply with the SCC but were incurred for one of the reasons stated in the corresponding definition.
It is the Project Manager who decides the above and if the Employer wishes to pay less than an amount certified they need to comply with the requirements of Y(UK) 2 in regard to the giving of a timely and compliant pay less notice, otherwise you are entitled to be paid the certified amount.
The fact you have not submitted the required records specified in the Works Information is essentially a breach of your contractual obligations. The problem is addressing this 'breach' as the apparent remedy under the contract seems to be clause 25.2, which relates to any cost incurred by the Employer, which doesn't appear to apply in your case.
It is the Project Manager who decides the above and if the Employer wishes to pay less than an amount certified they need to comply with the requirements of Y(UK) 2 in regard to the giving of a timely and compliant pay less notice, otherwise you are entitled to be paid the certified amount.
The fact you have not submitted the required records specified in the Works Information is essentially a breach of your contractual obligations. The problem is addressing this 'breach' as the apparent remedy under the contract seems to be clause 25.2, which relates to any cost incurred by the Employer, which doesn't appear to apply in your case.