Duplicate Multisite Primary Site Permalinks/Images Question

If you duplicate the primary multisite with such plugins like mu duplicator and have every option checked to copy including images, would you run into a problem with wordpress getting confused?

I duplicated my primary site when i made a subsite and my images in some widgets in my menu disappeared and in my ubermenu plugin i was using.

Is it safe to duplicate media as well when it comes to creating subsites in the same wordpress install? Thanks