Individualisation of products and ever-shorter product lifecycles require manufacturing companies to quickly reconfigure their production and adapt to changing requirements. While most of the existing literature focuses on organisational structures or hardware requirements for reconfigurability, requirements and best practices for logical reconfigurations of automated production systems are only sparsely covered. In practice, logical system reconfigurations require adjustments to the software, which is often done manually by experts. With the ongoing automation and digitisation of manufacturing systems in the context of Industry4.0, the need for automated software reconfigurations is increasing. However, heterogeneous and proprietary technologies in the field of industrial automation pose a hurdle to overcome for generally applicable approaches for logical reconfigurations in the industrial domain. Therefore, this paper reviews available technologies that can be used to solve the problem of automated software reconfigurations. For this purpose, an architecture and a procedure are proposed on how to use these technologies for automatic adaptation and virtual commissioning of control software in industrial automation. To demonstrate the interoperability of the approach, collective cloud manufacturing is used as a composing platform. The presented approach further includes a domain-specific capability model for the specification of software artefacts to be generated, allowing jobs to be described and matched on the platform. The core element is a code generator for generating and orchestrating the control code for process execution using the reconfigurable digital twin as a validator on the platform. The approach is evaluated and demonstrated in a real-world use case of a modular disassembly station.