We consider compact elliptic four-folds whose fiber ceases to be flat over Riemann surfaces of genus g in the base. We show that those contributions generically lead to non-trivial threeform cohomology proportional to g and the number of non-flat fiber components. These non-flat components can be viewed as compactifications of non-flat three-folds where they correspond to superconformal matter theories. Moreover we show, that one can perform conifold transitions that remove those non-flat fibers, corresponding to non-flat fibers in codimension three and second to birational base changes. The former phase is interpreted as a non-perturbative gauge invariant fourpoint coupling and the second one is closer to a classical 4D Coulomb branch.