Along with the growth of communication and satellite industry, the importance of satellite antenna evaluation is increasing. Particularly Communication On The Move (COTM) terminal antenna, including the communication between new types of constellations on LEO and MEO, requires tracking accuracy test for the communication on moving vehicles. The conventional test facilities are locally fixed and lack flexibility. To make the antenna measurement more accessible, we are developing a methodology for in-situ measurement by introducing multiple Unmanned-Aerial-Vehicles (UAVs) system with RF payload. Thanks to the dynamic flexibility of UAVs, this system can flexibly change the test configuration on site and make new test scenarios available, such as emulating the orbit of non-GEO satellites during the measurement. However, one of the challenges of the proposed system is the additional uncertainties during the measurement due to the mobility of UAVs. To overcome this challenge, we design recursive stochastic filtering and fusion approaches, and evaluate their estimation performance via numerical simulations. By introducing stochastic filter and fusion algorithms, the effect of error is mitigated, and better accuracy can be achieved compared to an existing method. This project is performed in collaboration with Cranfield University in the UK and QuadSAT in Denmark.