This paper presents a new approach from a certification standpoint toward the fault-tolerant control (FTC) strategies used to accommodate failures of a Remotely Piloted Aircraft System (RPAS) in non-conventional aerodynamic configuration. The reference aircraft of this paper is the ATLANTE RPA, which has a V-tail. A novel review of the most common accidents and incidents in general and commercial aviation, and in the RPAS sector, has been conducted in order to check the relevance of the proposed failures and the flight phase where they most frequently happen. Damage scenarios are, on the one hand, one locked-in-place flaperon and, on the other hand, propulsion system failure resulting in a gliding flight condition. This second scenario is an original contribution of this paper. The proposed FTC is based on the multiple model switching and tuning technique, and then a classical control is applied to each model in order to ensure the certification criteria. In the case of the propulsion system failure model, a new architecture with airspeed-on-elevator control law is proposed. This controller has been tested using a novel guidance law during the gliding, final approach, and landing phases making use of a flight simulator developed for the ATLANTE RPA. The results obtained highlight the concordance between the regulation requirements and the results for both proposed failures, making it possible for the aircraft to meet the certification requirements, while maintaining a safe condition after failures.