Some counties are overly strict when it comes to retro-active permits, and if it is not up to code, you may still be required to remove modifications, or they may come up with their own plan.

What county/city (if you feel comfortable sharing that) is the property located in?

The other user that responded is correct (u/Salmundo), ingress/egress may be a real concern. As there are specific rules for windows, escape routes (fire safety), and the like.