We build on our construction of Hopf algebroids from noncommutative calculi under the further assumption of surjectivity for the calculus. We also introduce the notions of Hopf ideals and isotopy quotients for arbitrary Hopf algebroids. Using these ingredients, we prove a Riemann-Hilbert correspondence for digraphs, by showing that the groupoid algebra of the fundamental groupoid of a digraph is isomorphic to the isotopy quotient of the Hopf algberoid corresponding to flat connections over the digraph.