Probabilistic forecasts are regarded as the highest achievable goal when predicting earthquakes, but limited information on stress, strength, and governing parameters of the seismogenic sources affects their accuracy. Ensemble data-assimilation methods, such as the Ensemble Kalman Filter (EnKF), estimate these variables by combining physics-based models and observations.While the EnKF has demonstrated potential in perfect model experiments using earthquake simulators governed by rate-and-state friction (RSF) laws, challenges arise from the non-Gaussian distribution of state variables during seismic cycle transitions. This study investigates the Adaptive Gaussian Mixture Filter (AGMF) and the Particle Flow Filter (PFF) as alternatives for improved stress and velocity estimation in earthquake sequences compared to Gaussian-based methods like the EnKF. We test the AGMF and the PFF's performance using Lorenz 96 and Burridge-Knopoff 1D models which are, respectively, standard simplified atmospheric and earthquake models. We test these models in periodic, and aperiodic conditions, and analyze the impact of assuming Gaussian priors on the estimates of the ensemble methods. The PFF demonstrated comparable performance in chaotic scenarios, yielding lower RMSE for the estimates of the Lorenz 96 models and stronger resilience to underdispersion for the Burridge-Knopoff 1D models. This is vital given the limited and sparse historical earthquake data, underscoring the PFF's potential in enhancing earthquake forecasting. These results emphasize the need for careful data assimilation method selection in seismological modeling