Suspensions of sedimenting slender fibres in a viscous fluid are known to be unstable to fluctuations of concentration. In this paper we develop a theory for the role of fibre flexibility in sedimenting suspensions in the asymptotic regime of weakly flexible bodies (large elasto-gravitation number). Unlike the behaviour of straight fibres, individual flexible filaments rotate as they sediment, leading to an anisotropic base state of fibre orientations in an otherwise homogeneous suspension. A mean-field theory is derived to describe the evolution of fibre concentration and orientation fields, and we explore the stability of the base state to perturbations of fibre concentration. We show that fibre flexibility affects suspension stability in two distinct and competing ways: the anisotropy of the base state renders the suspension more unstable to perturbations, while individual particle self-rotation acts to prevent clustering and stabilizes the suspension. In the presence of thermal noise, the dominant effect depends critically upon the relative scales of flexible fibre self-rotation compared to rotational Brownian motion.