Factory compliances

I have set up a company and am in the process of registering under the factories act (Maharashtra).  The factory (on rent)  comprises of the legal area and an illegally built addition.

I am registering the layout of the legally built  area only, the illegal part is a seperate building but in the same complex.

A point of view would be welcome as regards potential down the line issues.  The factory is situated in Vasai/Virar