Are you sure you have a Certificate of Occupancy as Jersey City only requires them for specific reasons (i.e. new construction, if you purchase the building from the city, if the owner requests, or if there is a change of use, etc.). They do, however, always require a Smoke Certificate which might be confusing you. As I have no idea what your situation I am taking a stab of what might have happened so I will apologize in advance if I have any way insulted you.
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I hope this helps!