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In the present paper, we use a coarse-graining approach to investigate the nonlinear redistribution of free energy in both position and scale space for weakly collisional magnetised plasma turbulence. For this purpose, we use high-resolution numerical simulations of gyrokinetic (GK) turbulence that span the proton-electron range of scales, in a straight magnetic guide field geometry. Accounting for the averaged effect of the particles' fast gyro-motion on the slow plasma fluctuations, the GK approximation captures the dominant energy redistribution mechanisms in strongly magnetised plasma turbulence. Here, the GK system is coarse-grained with respect to a cut-off scale, separating in real space the contributions to the nonlinear interactions from the coarse-grid-scales and the sub-grid-scales (SGS). We concentrate on the analysis of nonlinear SGS effects. Not only that this allows us to investigate the flux of free energy across the scales, but also to now analyse its spatial density. We find that the net value of scale flux is an order of magnitude smaller than both the positive and negative flux density contributions. The dependence of the results on the filter type is also analysed. Moreover, we investigate the advection of energy in position space. This rather novel approach for GK turbulence can help in the development of SGS models that account for advective unstable structures for space and fusion plasmas, and with the analysis of the turbulent transport saturation.