This paper presents an adaptive fault-tolerant resource allocation protocol tailored for FlyNet, a dynamic aerial network characterized by its mobility and three-dimensional operational space. Addressing the challenges of network partitioning and resource allocation in aerial networks, the proposed algorithm dynamically adjusts to the network's changing topology, ensuring consistent and efficient resource management. Through robust fault tolerance mechanisms, the protocol enhances FlyNet's reliability, maintaining seamless communication and optimal resource utilization even amid node mobility and disruptions. Simulation results demonstrate the algorithm's effectiveness in adapting to dynamic environments, maximizing resource utilization, and minimizing communication delays.