Unmanned aerial vehicles (UAVs) suffer from sensor drifts in GPS denied environments, which can cause safety issues. To avoid intolerable sensor drifts while completing the time-critical coordination task for multi-UAV systems, we propose a safety constrained bi-level control framework. The first level is the time-critical coordination level that achieves a consensus of coordination states and provides a virtual target which is a function of the coordination state. The second level is the safety-critical control level that is designed to follow the virtual target while adapting the attacked UAV(s) at a path re-planning level to support resilient state estimation. In particular, the time-critical coordination level framework generates the desired speed and position profile of the virtual target based on the multi-UAV cooperative mission by the proposed consensus protocol algorithm. The safety-critical control level is able to make each UAV follow its assigned path while detecting the attacks, estimating the state resiliently, and driving the UAV(s) outside the effective range of the spoofing device within the escape time. The numerical simulations of a three-UAV system demonstrate the effectiveness of the proposed safety constrained bi-level control framework.