Manufacturing companies are facing new market demands, mostly driven by global competition and digitalization. In this context, more efficient, flexible, adaptable and evolvable mechatronic and manufacturing systems are required, which enable quick adjustments to the production in order to address (all these) market changes. However, production idle times due to such re-configurations and adaptations might be costly. In this paper, a live updates concept for Programmable Logic Controllers (PLCs) is presented. The proposed design employs a Petri net runtime engine, in which the executed functional program (the Petri net model with its interpretation) is updated while running, without system shutdown and restart being needed. To this end, a quarantine-mode execution and monitoring approach is used for the new PLC program functional validation. A reconfigurable Vernadat machine case study is also presented.