Just to update. I talked with a land-use planner. Due to conflicts she could not take me on but did give some advice. My best chance is the utility company getting back to me about when the 3 units were first billed with separate meters. This has been troublesome due to the city utility company not actually getting back with me so far.
If it ends up being an illegal-non conforming then I plan on appealing at a board meeting. Not sure my argument will stand a chance but rentals are badly needed in this area and it has been used as an illegal non-conforming triplex in the past.
If this doesn't work then I plan on arguing it being a legal non-conforming duplex, keep the 3 units, but just combine the utilities for two of the units.
My last resort would be if the house was zoned as a single-family. I would combine them all on one meter, keep the three units, and put utilities in my name. From what I am told, this option depends on what defines a single-family in my area and how many non-related people can live in a house together.
Has anyone heard of the board of appeals in a city going against the zoning law or allowing special permission for a particular use? Is this common?