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In nowadays production, fluctuations in demand, shortening product life-cycles, and highly configurable products require an adaptive and robust control approach to maintain competitiveness. This approach must not only optimise desired production objectives but also cope with unforeseen machine failures, rush orders, and changes in short-term demand. Previous control approaches were often implemented using a single operations layer and a standalone deep learning approach, which may not adequately address the complex organisational demands of modern manufacturing systems. To address this challenge, we propose a hyper-heuristics control model within a semi-heterarchical production system, in which multiple manufacturing and distribution agents are spread across pre-defined modules. The agents employ a deep reinforcement learning algorithm to learn a policy for selecting low-level heuristics in a situation-specific manner, thereby leveraging system performance and adaptability. We tested our approach in simulation and transferred it to a hybrid production environment. By that, we were able to demonstrate its multi-objective optimisation capabilities compared to conventional approaches in terms of mean throughput time, tardiness, and processing of prioritised orders in a multi-layered production system. The modular design is promising in reducing the overall system complexity and facilitates a quick and seamless integration into other scenarios.