@John Warren Yes, it is legal nonconforming. I ran the scenario by another company and I received the same conclusion - FHA will not accept it.
The fact that the city stated the property could not be rebuilt as is if destroyed seems to be the underlying issue for FHA. It would have to be rebuilt as a single family (not a duplex) if destroyed.
I'm assuming the city made this statement because they want the property to comply with current zoning ordinances if it had to be rebuilt. The property can continue its existing use.
I am not sure why rebuilding as a single family if destroyed makes a difference since my mortgage broker confirmed I would qualify for the property without factoring in the rental income (i.e. if this was a single family at the same purchase price I would still be able to afford the property). If I can afford to pay the mortgage and the city does not have an issue with the property continuing its existing use, then why would FHA have an issue.
Have you recently closed using FHA on a legal nonconforming property? Maybe the requirements recently changed.