The Internet of Things (IoT) and Industrial Internet of Things (IIoT) trends, where high connectivity is envisioned, are giving rise to new applications, services, and paradigms, such as smart cities. Due to this connectivity and information sharing features, security, and privacy protection mechanisms need to be implemented, which may become obsolete at some future time. Software updates are, then, crucial. However, software updates requiring system shutdown and restarts might not be acceptable from the business and service point of view when high availability is demanded. In this paper, a mixed-criticality software architecture and design for a building energy management system, built upon the Cetratus runtime framework, is presented, where partitioning techniques are employed to ensure temporal and spatial isolation. Through this framework, software updates are dynamically accomplished, without the need for system shutdown and restarts. A live patching example is also presented, where customers privacy is enhanced by means of homomorphic encryption.