From simple rules like permits to outright bans so that is a huge risk IMHO.

Our local towns and rental assistance programs really appreciate those that try to work with their tenants which has helped me several times through easier permitting processes.

NYC DOB considers a shelter a 'community facility with sleeping quarters' and may require a special permit for this use.Thanks Abel, You provided me with the right search terms to dig deeper. 

And I have below clause in the leaseRental Application: Only those people indicated on Tenant’s rental application are permitted to reside at the Premises, with the exception of any minor children born to, or adopted by, Tenant.

Does that mean I'm all set and can break it up in to separate units, or do I need to get a permit or rezone or other things?

Duplex Development Made Easy - SB 9 permits property owners to convert single-family lots into duplexes.

I have 10 water front lots on a trout river in WNC with mountain views, they are cleared. i have the site permit, i have the well and septic permits.

Contract does state: "Nothing in this Contract shall be interpreted to permit Seller to provide false, misleading, or fraudulent information to Buyer." 

If they are separate, permits would have been pulled and the city will have records of those permits.  

Depending on the construction, you have to do major upgrades on electric, plan for plumbing for apartments which may not be permitted in the area for the sewer or septic.