The ensemble Kalman filter (EnKF) is widely adopted for sequential data assimilation, but fails for solutions with discontinuities, such as shocks in compressible flows. For ensembles with uncertainty in discontinuity location, the EnKF analysis can lose physical consistency, which can be viewed through three lenses: (i) bimodal pointwise statistics in the forecast ensemble, (ii) mixed-sign analysis weights in the affine superposition of forecast members, and (iii) spatially distributed Kalman-gain profiles that modify the state around a discontinuity rather than translating it coherently. In order to preserve flow features in the analysis state and, as such, maintain physical consistency, a feature-preserving latent-EnKF is introduced. The proposed method performs the ensemble update in a low-dimensional latent space learned by a coordinate-conditioned auto-decoder. The latent representation retains near-Gaussian ensemble statistics and provides coordinates in which flow features vary coherently across the forecast ensemble. The EnKF updates performed on the latent codes are decoded into coherent changes in the represented flow features, translating shocks through coordinate morphing rather than superposing them at displaced locations. The corresponding Kalman-gain profiles generated by the latent-EnKF exhibit an approximately step-like variation across the discontinuities, allowing the fronts to translate while preserving sharp features and monotonicity. Sod shock-tube, Mach~2 shock-cylinder, and immersed-body shape-inference tests with sparse, noisy observations demonstrate accurate recovery of shocks and contact discontinuities without spurious oscillations.

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