Separation of network control from devices in Software Defined Network (SDN) allows for centralized implementation and management of security policies in a cloud computing environment. The ease of programmability also makes SDN a great platform implementation of various initiatives that involve application deployment, dynamic topology changes, and decentralized network management in a multi-tenant data center environment. Dynamic change of network topology, or host reconfiguration in such networks might require corresponding changes to the flow rules in the SDN based cloud environment. Verifying adherence of these new flow policies in the environment to the organizational security policies and ensuring a conflict free environment is especially challenging. In this paper, we extend the work on rule conflicts from a traditional environment to an SDN environment, introducing a new classification to describe conflicts stemming from cross-layer conflicts. Our framework ensures that in any SDN based cloud, flow rules do not have conflicts at any layer; thereby ensuring that changes to the environment do not lead to unintended consequences. We demonstrate the correctness, feasibility and scalability of our framework through a proof-of-concept prototype.