Astronomical observations of neutron stars probe kilometer scales, while the underlying nuclear interactions act on femtometer scales, requiring effective models to bridge this gap. In the inner crust, a lattice of nuclei interacts strongly with superfluid neutrons. By neglecting explicit neutron and proton degrees of freedom, one can capture the essential physics through an effective nuclear mass that emerges from these interactions. Using generalized Skyrme energy-density functionals of the Brussels–Montreal family, we study the nonequilibrium dynamics of a nucleus across different crustal layers to compute this effective mass. We identify three distinct dissipation mechanisms: phonon emission, Cooper-pair breaking, and vortex-ring creation. The last mechanism is particularly interesting in the context of a microscopic source of glitches.