The manufacturing of composite structures can lead to material defects. Some of these defects, due to their small size, can go undetected by current non-destructive testing techniques; especially in very large and geometrically complex components. Therefore, it is of paramount importance to design composite components to resist defects by accounting for them as early as possible. Topology optimisation is a methodology whereby complex features, such as cracks and debonds, can be accounted for in the design. Therefore, this work proposes a new approach for the design of very large composite structures. This new approach is enabled by a solid shell element formulation with boundary tracking capabilities (through the floating node and the level-set methods) and optimisation capabilities (through design sensitivity analysis of an energy release rate objective function). Furthermore, this work proposes a new algorithm and modelling workflow that has the ability to handle large multi-scale models. The proposed methodology shows advantages as the ability to track the topology explicitly, and the ability to increase defect tolerance of the design. This works shows the new methodology is capable of handling complex structures, such as a multi-scale stringer run-out model from an aircraft wing-box, while a kissing bond defect is present.