This problem is common with homesites where the underlying land has been rezoned for commercial use, although there is no demand for this commercial use and the existing improvements represent the highest and best use as improved. Thoughts?
While zoning is a factor, it is not the only one that determines HBU. In your example, if there is no demand for commercial, the HBU probably remains residential and the land will be valued accordingly. There's a lot of land with comm/indust zoning in this area with corn growing on it these days. HBU= Agricultural. In the current market, zoning adds little or no value.
Most of my work is R/W and in your example, the land would be valued and compensated as residential, and if appropriate, the residential improvements would be damaged and compensated accordingly. (For example, $100k property, $75K imp/$25K land)
If the HBU of the same parcel is commercial and the residential improvements add no value, the acquired land will be compensated as commerical but there would be no compensation for setback damages to the improvements, even if the property remains residential in use. ($100K land, $0 improvments contrib.value.)
Or it could be transitional and since any damage compensation is based on the contributory value of the residential improvements, the damage amount will be based on a reduced improvements value. ($75K land, $25K imp.)
At least that's the way the State of Indiana accepts/requires.