This paper addresses software design for cyber-physical automation systems that enables invariant properties of the physical system in case of software reallocation to different hardware. The proposed approach is based on the distributed reference architecture of IEC 61499 standard enhanced with a time-stamping mechanism. It is demonstrated that the proposed approach complements the abilities of IEC 61499 to maintain correct causality of distributed system execution with improved performance of physical system property called cyber-physical agnosticism. The time-stamped event semantics of IEC 61499 is introduced and mapped to the PTIDES execution model of Ptolemy II. We have experimentally validated that changing the model of computation in distributed automation to a time-stamped event-driven one can bring substantial improvements in flexibility and reconfigurability of cyber-physical automation systems.