The insurance company are trying to make a case that the car (or the engine) will be better after repair than before the car was flood damaged.
If, for example the engine had 60,000kms before the flood and repairers can only find a brand new engine as a replacement, then your insurer is entitled to recoup the cost ("notional" ?) of the 60,000kms as to not do so would leave you better off. Does that make sense?
All insurers have a "no betterment" condition; it is fundamental to their business. The purpose of insurance is to restore you to the state you were in before accident / flood