Here in Michigan, I've ran into an issue of a 2 unit that has been functioning as a 3 unit for 19 years. It has separate meters. I bought this spring, and began renovating. When I went to rent, several neighbors called the City and reported me.
They claimed I am devaluing their property values. Not remotely the case because of my investment then raising rents $500 / unit. I also refused to accept Section 8. They also made comments I will rent to dozens of people, or rent to someone and allow their "nephew" to attend school in the district.
Another person said it wasn't fair for me to make more money than them and I just bought there.
This property sat for at least 3 years with several blight violations, that I have addressed. It appears several neighbors have started a whisper campaign and are now using the local building enforcement to stop me from renting period. I told the building inspectors I have no issues bringing things up to code, but I find the property owners concern around my new property disingenuous considering how long the property operated as 3 units, had 3 meters, and the numerous violations that were unaddressed. This property sat on the market 5 years, and several people tried to buy it, but we were willing to pay more money to the seller. I estimate hundreds of people had been inside the property between all the sales attempts. I know several neighbors were aware on the interior condition.
Based on length of operations can I request a variance? Its obviously was operated as a 3 unit and zoned a 2 unit. But going on 19 years, I was able to verify with records from energy company, this is surely a grandfathered issue.
Have you talked to the zoning admin? That's what you should do. Ideally, you should have got the ok before purchasing. If you weren't able to get an approval, that would have impacted the price you'd be willing to pay.