In this paper, a novel framework for cooperative estimation of formation flight of unmanned vehicles subject to presence of actuator faults is proposed. This framework is developed based on the notion of sub-observers where within a group of sub-observers each sub-observer is estimating certain states that are conditioned on a given input, output, and state information. We model the overall estimation process by a weighted estimation (WE) digraph. By selecting an appropriate path in the weighted estimation digraph, an assigned supervisor can select and configure a set of sub-observers to successfully estimate all the system states. In presence of large disturbances, noise, and faults certain sub-observers may become invalid (or unreliable), and consequently the supervisor reconfigures the set of sub-observers by selecting a new path in the estimation digraph such that the impacts of these anomalies are confined to only the local estimators. This will prevent the propagation of the uncertainties on the estimation performance of the entire formation flight system. Simulations are conducted on a five satellite formation flight system in deep space where the results confirm the validity of our analytical work.