In the paper a Petri net based approach for modeling dynamically modifiable embedded real-time systems is presented. The presented work contributes to the extension of a Petri net based design methodology for distributed embedded systems towards the handling of dynamically modifiable systems. Extensions to the underlying High-Level Petri net model are introduced that allow for dynamic modifications of a net at run-time. Furthermore, a simulation tool for the resulting self-modifying net model is outlined. The tool has been designed to simulate the execution of a dynamically modifying Petri net on a simplified model of a hardware platform which is dynamically modifying as well.