Data assimilation algorithms are used to estimate the states of a dynamical system
using partial and noisy observations. The ensemble Kalman filter has become a
popular data assimilation scheme due to its simplicity and robustness for a wide
range of application areas. Nevertheless, this filter also has limitations due to
its inherent assumptions of Gaussianity and linearity, which can manifest
themselves in the form of dynamically inconsistent state estimates. This issue is
investigated here for balanced, slowly evolving solutions to highly oscillatory
Hamiltonian systems which are prototypical for applications in numerical weather
prediction. It is demonstrated that the standard ensemble Kalman filter can lead
to state estimates that do not satisfy the pertinent balance relations and
ultimately lead to filter divergence. Two remedies are proposed, one in terms of
blended asymptotically consistent time-stepping schemes, and one in terms of
minimization-based postprocessing methods. The effects of these modifications
to the standard ensemble Kalman filter are discussed and demonstrated
numerically for balanced motions of two prototypical Hamiltonian reference
systems.