At what point does a duplex become a third apartment in a two family dwelling?

So let’s say you have a 3 story house with no C of O, which the DoB sees is as a B3-2, 2 family converted from a single (and it’s taxed as a 2 fam as well). There are two electrical meters, one for the top floor which is a separate apartment, and one for the bottom two floors which are a ‘duplex’. But the duplex (parlor floor + English basement) is separated/connected by a staircase with a door in front on parlor floor, which (when coming up the stairs from the lower part) takes you to the parlor floor hallway which has another two doors (one door to the front hall where the front door is and one door to a rear bedroom). In other words, the bottom could be a separate apartment. With no kitchen. (There are only two kitchens in the entire structure, one of the top floor and one on the parlor floor.) I’m trying to determine what to do about the duplex. Getting a C of O for a 3 is too costly. So what I’m thinking I might do is, I live in the parlor floor and use the basement apartment for short term vacation rentals. And the rest of the time use it as my own space. My question to you is, at what point does this start to look like “it’s being used illegally as a three family multiple dwelling” in the eyes of the city? Does the presence of a lockable door cause this? Is there somewhere that I can read about what I can and cannot do? What alterations I can and cannot do? I’ve been unsuccessful in my online research and I’m not sure I want to use an attorney to answer this. I’m feeling like I should talk to an architect for advice, though.