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We study global anomalies of discrete gauge symmetries in six-dimensional supergravities and their realizations in F-theory. We explicitly construct a discrete Green-Schwarz mechanism that depends on the choice of a coupling constant and on a certain quadratic refinement in differential cohomology. By geometrically engineering theories with $G=\mathbb{Z}_3$ gauge symmetry and no tensor multiplets, we observe that a particular choice of the quadratic refinement is singled out in F-theory. This implies new Swampland constraints on the discrete charge spectra of 6d supergravities. On the other hand, the discrete Green-Schwarz coupling depends on the geometry of the Calabi-Yau. We use anomaly inflow to relate this to a 't Hooft anomaly of the induced global symmetry in the worldsheet theories of non-critical strings. Using topological symmetry lines, we further relate this anomaly to the modular properties of twisted-twined elliptic genera. We then argue that the latter are encoded in the A-model topological string partition functions on different torus fibrations that are equipped with a flat torsional B-field. This allows us to derive a geometric expression for the global discrete anomaly in terms of the height-pairing of a multi-section on a genus one fibered Calabi-Yau.