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In this paper we devise and analyze a mixed finite element method for a modified Cahn-Hilliard equation coupled with a non-steady Darcy-Stokes flow that models phase separation and coupled fluid flow in immiscible binary fluids and diblock copolymer melts. The time discretization is based on a convex splitting of the energy of the equation. We prove that our scheme is unconditionally energy stable with respect to a spatially discrete analogue of the continuous free energy of the system and unconditionally uniquely solvable. We prove that the phase variable is bounded in \(L^\infty \left(0,T,L^\infty\right)\) and the chemical potential is bounded in \(L^\infty \left(0,T,L^2\right)\) absolutely unconditionally in two and three dimensions, for any finite final time \(T\). We subsequently prove that these variables converge with optimal rates in the appropriate energy norms in both two and three dimensions.