Software rejuvenation protects cyber-physical systems (CSPs) against cyber attacks on the run-time code by periodically refreshing the system with an uncorrupted software image. The system is vulnerable to attacks when it is communicating with other agents. Security is guaranteed during the software refresh and re-initialization by turning off all communication. Although the effectiveness of software rejuvenation has been demonstrated for some simple systems, many problems need to be addressed to make it viable for real applications. This paper expands the scope of CPS applications for which software rejuvenation can be implemented by introducing architectural and algorithmic features to support trajectory tracking. Following each software refresh, while communication is still off, a safety controller is executed to assure the system state is within a sufficiently small neighborhood of the current point on the reference trajectory. Communication is then re-established and the reference trajectory tracking control is resumed. A protected, verified hypervisor manages the software rejuvenation sequence and delivers trusted reference trajectory points, which may be received from untrusted communication, but are verified using an authentication process. We present the approach to designing the tracking and safety controllers and timing parameters and demonstrate the secure tracking control for a 6 DOF quadrotor using the PX4 jMAVSim quadrotor simulator. The concluding section discusses directions for further research.