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Over the past years, the amount of detected multi-planet systems significantly grew, an important sub-class of which being the compact configurations. A precise knowledge of them is crucial to understand the conditions with which planetary systems form and evolve. However, observations often leave these systems with large uncertainties, notably on the orbital eccentricities. This is especially prominent for systems with low-mass planets detected with Radial Velocities (RV), the amount of which is more and more important in the exoplanet population. It is becoming a common approach to refine these parameters with the help of orbital stability arguments. Such dynamical techniques can be computationally expensive. In this work we use an alternative procedure faster by orders of magnitude than classical N-body integration approaches. We couple a reliable exploration of the parameter space with the precision of the Numerical Analysis of Fundamental Frequencies (NAFF, Laskar 1990) fast chaos indicator. We also propose a general procedure to calibrate the NAFF indicator on any multi-planet system without additional computational cost. This calibration strategy is illustrated on HD 45364, in addition to yet-unpublished measurements obtained with the HARPS and CORALIE high-resolution spectrographs. We validate the calibration approach on HD 202696. We test the performances of this stability-driven approach on two systems with different architectures. First we study HD 37124, a 3-planet system composed of planets in the Jovian regime. Then, we analyse HD 215152, a compact system of four low-mass planets. We demonstrate the potential of the NAFF stability-driven approach to refine the orbital parameters and planetary masses. We stress the importance of undertaking systematic global dynamical analyses on every new multi-planet system discovered.