Nowadays, great efforts of ongoing research are devoted to hybrid-electric propulsion technology that offers various benefits, such as reduced noise and pollution emissions and enhanced aircraft performance and fuel efficiency. The ability to estimate the performance of an aircraft in any flight situation in which it may operate is essential for aircraft development. In the current study, a simulation model was developed that allows estimating the flight performance and analyzing the mission of a fixed-wing multi-rotor Unmanned Aerial Vehicle (UAV) with a hybrid electric propulsion system (HEPS), with both conventional and Vertical Takeoff and Landing (VTOL) capabilities. The control is based on the continuous specification of pitch angle, propulsion thrust, and lift thrust to achieve the required conditions of a given flight segment. Six different missions were considered to analyze the effect of control parameters exhibiting the most influence on the UAV mission performance. An appropriate set of control parameters was selected through a multidimensional parametric study. The results show that the control parameters, if not well tuned, affect the mission performance: for example, in the deceleration transition, a longer time to reduce the cruise speed to stand still may be the result because the controller struggles to adjust the pitch angle. In addition, the implemented methodology captures the effects of transient maneuvers, unlike typical quasi-static analysis without the complexity of full simulation models.