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We study a slow-fast system of coupled two- and three-dimensional Navier-Stokes equations in which the fast component is perturbed by an additive fractional Brownian noise with Hurst parameter . The system is analyzed using rough path theory, and the limiting behaviour strongly depends on the value of . We prove convergence in law of the slow component to a Navier-Stokes system with an additional Itô-Stokes drift when . In contrast, for , the limit equation features only a transport noise driven by a rough path.

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