Answered: Is the project manager entitled to deduct more advance payment repayment from IPCs than what is stipulated in the contract?

Assuming you have Secondary Option X14 and the amount to be re-paid in instalments is stated in the Contract Data as $128,000 per month (assumed this is your assessment interval), then the Project Manager is obliged to deduct the amount stated.  As this is information stated in the Contract Data, then it can only be changed by a Deed of Variation between the parties to the contract.

Similarly, the Project Manager could not decide, for no particular reason other than his own opinion, to increase the retention percentage from 3% to 5%, if it is stated in the Contract Data to be 3%.