This paper presents the development and implementation of a multi-UAV system focused on coverage path planning on multiple separated areas capable of re-planning the collective mission in case of unexpected events. For this purpose, we present a distributed-centralized architecture that uses heuristic and computationally efficient methods to perform the planning/re-planning and decision-making tasks during the control of the mission execution. We performed a computational evaluation of the algorithms, comparing them with other proposals, together with experiments in simulated and real flights. The results show that the system can distribute tasks equitably among the aircraft in an efficient way, even in the middle of the flight, when facing unexpected events; and show a higher computational efficiency when compared to multiple proposals in the state of the art.