The anomalous Hall, Nernst and thermal Hall coefficients of Fe$_{3-x}$GeTe$_2$ display several features upon cooling, like a reversal in the Nernst signal below $T = 50$ K pointing to a topological transition (TT) associated to the development of magnetic spin textures. Since the anomalous transport variables are related to the Berry curvature, a possible TT might imply deviations from the Wiedemann-Franz (WF) law. However, the anomalous Hall and thermal Hall coefficients of Fe$_{3-x}$GeTe$_2$ are found, within our experimental accuracy, to satisfy the WF law for magnetic-fields $mu_0H$ applied along its inter-layer direction. Surprisingly, large anomalous transport coefficients are also observed for $mu_0H$ applied along the planar emph{a}-axis as well as along the gradient of the chemical potential, a configuration that should not lead to their observation due to the absence of Lorentz force. However, as $mu_0H$ $|$ emph{a}-axis is increased, magnetization and neutron scattering indicate just the progressive canting of the magnetic moments towards the planes followed by their saturation. These anomalous planar quantities are found to not scale with the component of the planar magnetization ($M_{|}$), showing instead a sharp decrease beyond $sim mu_0 H_{|} = $ 4 T which is the field required to align the magnetic moments along $mu_0 H_{|}$. We argue that locally chiral spin structures, such as skyrmions, and possibly skyrmion tubes, lead to a field dependent spin-chirality and hence to a novel type of topological anomalous transport. Locally chiral spin-structures are captured by our Monte-Carlo simulations incorporating small Dzyaloshinskii-Moriya and biquadratic exchange interactions.
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