Embedded systems are usually an integral component of a larger system and are used to control and/or directly monitor this system by using special hardware devices. The complexity of the whole system, which the embedded control system monitors, increases steadily. Consequently, the initial version of the control software that is used at the time of deployment may be inadequate and may need to be updated. Often this requires the whole system to be shut down to have the software replaced. This is not a desirable solution. In this work, we propose a non-blocking mechanism embedded into an infrastructure for RTLinuxPro for deterministic replacement of system functionality, task timing, and data-flow for hard real-time systems. We explain the mechanism, discuss its implementation using RTLinuxPro, and present a case study of a stop watch in which we replace single functionality and timing behavior at runtime without compromising the timeliness of tasks or the correctness of the output values. The contribution is to show how such a mechanism can work, how it can be implemented, and what problems arise in multi-mode real-time applications.