Any change in a council's classification of properties can have some impact on property values. Nevertheless, councils normally give due consideration to such impacts before introducing a system of flood risk classifications or any other classification system (e.g. bushfire risks, acid sulphate soil risk, etc).
If your property is suddenly classified as being in Flood Prone the real flood risks on your property have not changed, rather, present information regarding risk estimates has become more available for Council to inform decision making. A prospective purchaser of your property could have previously discovered this risk if they had made enquiries themselves.
Ultimately, the market determines the value of any residential property. Individual owners should seek their own valuation advice if they are concerned that the flood risk estimation may influence their property value.