If the Client has the right to audit any rates and they are found to not be compliant with the contract, presumably the Schedule of Cost Components, then they may also have the right to 'change' them, depending on what the contract says.
If the rates were stated in Contract Data Part 2, some information can be changed under the contract and some can't, except by deed of variation. Assuming they do have the right, then the risk lies with the Contractor to ensure that the rates are compliant with the requirements of the SCC and so any required changes, consequent to an audit, would be an allowable adjustment,
The fee percentage is not changed unless there is a mechanism in the contract to provide for this, which is common in relation to target cost contracts where the PWDD exceeds the total of the Prices. Otherwise the fee percentage does not change.