Yes there is something that protects the Contractor - it is called the contract!
63.1 states that if the instruction changes the Works Information then it should be based upon forecast defined cost (it states the switch point between actual and forecast being the instruction). Therefore the Contractor can base the assessment on what would have been reasonable to have expected the Subcontractor(including significant risk) to have incurred. That would not include inefficiencies that actually incurred. You assess likely cost and duration's that it should have taken them including allowance for risk which has a significant chance of occurring.
63.1 states that if the instruction changes the Works Information then it should be based upon forecast defined cost (it states the switch point between actual and forecast being the instruction). Therefore the Contractor can base the assessment on what would have been reasonable to have expected the Subcontractor(including significant risk) to have incurred. That would not include inefficiencies that actually incurred. You assess likely cost and duration's that it should have taken them including allowance for risk which has a significant chance of occurring.