It is not clear if the Contractor has followed the “reminder” process within your example. According to clause 62.6 of the contract, if the Project Manager has not responded to the quotation within two weeks (unless amended) then the Contractor MAY notify the Project Manager to this effect. Failure to respond to the reminder for a further two weeks would then mean that the quotation is “treated as having been accepted” i.e. deemed accepted.
The word MAY emphasizes that the Contractor does not have to do this, but then that the deemed acceptance does not kick in until two weeks after the reminder (when ever that is issued after the lack of initial response).
If this has been followed as described above then it is Implemented and it is full and final. The only remedy the Employer then has is adjudication, but that will only be for mathematical errors etc rather than subjective elements like what risk allowance should have been included or how many men should have been used.