Why would you re-zone it? If you did then you would have to start adhering to less ideal setbacks and requirements imposed by the City. Being non-conforming is ideal and simpler - the laws for grandfathering have been tested and hold up very well in court if it ever gets that far. The City should be letting you bring homes in and out using the existing setbacks without any issue - and if they’re not then the City is violating State laws. Hire a muni-lawyer with experience with grandfathering - they can speak with the City’s attorney to clear it up quickly. Grandfathering provisions are typically only removed from a property if the usage ceases for 12 or 18 months, which isn’t the case here, so it should not be a future issue for you or anyone in this scenario.
Read this: Putting the grandfathering concept to bed once and for all
If you want the deal to close simply keep it non-conforming, get a certificate of zoning, and follow all the other recommended steps in the MHU Due Diligence Manual.
Good luck.