We study the energy-density dynamics at finite momentum of the two-dimensional Kitaev spin-model on the honeycomb lattice. Due to fractionalization of magnetic moments, the energy relaxation occurs through mobile Majorana matter, coupled to a static $\mathbb{Z}_2$ gauge field. At finite temperatures, the $\mathbb{Z}_2$ flux excitations act as an emergent disorder, which strongly affects the energy dynamics. We show that sufficiently far above the flux proliferation temperature, but not yet in the classical regime, gauge disorder modifies the coherent low-temperature energy-density dynamics into a form which is almost diffusive, with hydrodynamic momentum scaling of a diffusion-kernel, which however remains retarded, primarily due to the presence of two distinct relaxation channels of particle-hole and particle-particle nature. Relations to thermal conductivity are clarified. Our analysis is based on complementary calculations in the low-temperature homogeneous gauge and a mean-field treatment of thermal gauge fluctuations, valid at intermediate and high temperatures.
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