In this paper, we consider the problem of controlling a rigid assembly of aerial vehicles under uncertainty. We consider the case when the positions of the vehicle modules in the assembly structure are unknown, but belong to a finite set. In addition, we consider that each module has only its own measurements available for feedback but not that of the whole assembly, so a decentralized control law is developed. We apply an adaptive switching control approach to control this uncertain system. Given a stabilizing controller for the case when there is no uncertainty, we show that the proposed adaptive approach achieves the control objective under uncertainty by presenting illustrative simulation examples; we provide a case study of a recently proposed novel modular flying system, namely a fractal tetrahedron assembly.