Air transportation traffic is progressively increasing over the years and dealing with it is an essential task to guarantee fluid flights in the future. Several works already indexed multiple aspects of aviation, among them, the E-MAN system. It introduced the sequencing of arriving traffic, starting from early stages of the En-route phase. This change facilitated the work for the approach controllers but also increased the workload of the En-route controllers. To handle that workload, controllers are now assisted by tools that consider the new constraints introduced by the arrival management system and propose advisories. From that same perspective, our project focuses on an algorithm for a helper tool that will combine both aspects of traffic sequencing in the En-route phase and conflict resolution. With this novel approach, we automatically generate near-to-optimal flight decisions, given that we can modify the speed and the flight level to respect the sequencing constraints and cut down potential conflicts. We categorize the problem as a mathematical optimization case. Thus, we describe a detailed mathematical model which covers all the aspects of the problem. This model gives a basis for the implementation of the flight optimizer. Later, we propose a solution based on a sliding window simulated annealing algorithm which reduces the complexity and takes into account uncertainties. Finally, we successfully test an implementation of the solution with real-life traffic data. It corresponds to flights within France going towards Paris CDG airport over a period of 24 hours. The results demonstrate a total conflicts resolution with satisfying compliance with sequencing constraints.