This paper presents a resilient, multi-layer architecture designed to ensure reliable autonomous operation of single and multiple quadcopters. The architecture leverages the resilient spacecraft executive to hierarchically organize trajectory-planning and flight-control functions, and integrates Simplex architectures at each level to provide safety assurance. A compound subsystem expands robustness by employing multiple candidate algorithms for planning and control, while a supervisory program adapts Simplex behavior based on system states and environmental conditions to enable high-level mission management. The architecture is evaluated in simulations involving environmental uncertainties, including varying wind and obstacles, within a bridge-inspection mission using both single- and multi-quadcopter configurations. Results show that the system maintains safe and effective operation across a wide range of conditions, demonstrating scalability for cooperative multi-agent tasks.