When using autonomous reconfigurable manufacturing system, that offers generic services, there is the possibility to dynamically manufacture a range of products using the same manufacturing equipment. Opportunities are created to optimally scale the production using reconfiguration means and automatically manufacture small amounts of unique or highly customizable products. Basically the result is a short time to market for new products. This paper discusses the problems that arise when manufacturing systems are reconfigured and the impact of this action on the entire system. The proposed software architecture and tooling makes it possible to quickly reconfigure a system without interference to other system, and shows how the reconfigured hardware can be controlled without the need to reprogram the software. Parameters that are required to control the new hardware can be added using a simple tool. As a result reconfiguration is simplified and can be achieved quickly by mechanics without reprogramming any systems. The impact is that time to market can be reduced and manufacturing systems can quickly be adapted to current real-time needs.