Complex aircraft systems are becoming a target for automation. For successful operation, they require both efficient and readable mission execution system. Flight control computer (FCC) units, as well as all important subsystems, are often duplicated. Discrete nature of mission execution systems does not allow small differences in data flow among redundant FCCs which are acceptable for continuous control algorithms. Therefore, mission state consistency has to be specifically maintained. We present a novel mission execution system which includes FCC state synchronization. To achieve this result we developed a new concept of Asynchronous Behavior Tree with Memory and proposed a state synchronization algorithm. The implemented system was tested and proven to work in a real-time simulation of High Altitude Pseudo Satellite (HAPS) mission.