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We study the dynamics of gauge-invariant scalar perturbations in cosmological scenarios with a modified Friedmann equation, such as quantum gravity bouncing cosmologies. We work within a separate universe approximation which captures wavelengths larger than the cosmological horizon; this approximation has been successfully applied to loop quantum cosmology and group field theory. We consider two variables commonly used to characterise scalar perturbations: the curvature perturbation on uniform-density hypersurfaces $ζ$ and the comoving curvature perturbation $\mathcal{R}$. For standard cosmological models in general relativity as well as in loop quantum cosmology, these quantities are conserved and equal on super-horizon scales for adiabatic perturbations. Here we show that while these statements can be extended to a more general form of modified Friedmann equations similar to that of loop quantum cosmology, in other cases, such as the simplest group field theory bounce scenario, $ζ$ is conserved across the bounce whereas $\mathcal{R}$ is not. We relate our results to approaches based on a second order equation for a single perturbation variable, such as the Mukhanov-Sasaki equation.