We calculate the generating functions of BPS indices using their modular properties in Type II and M-theory compactifications on compact genus one fibered CY 3-folds with singular fibers and additional rational sections or just $N$-sections, in order to study string dualities in four and five dimensions as well as rigid limits in which gravity decouples. The generating functions are Jacobi-forms of $Gamma_1(N)$ with the complexified fiber volume as modular parameter. The string coupling $lambda$, or the $epsilon_pm$ parameters in the rigid limit, as well as the masses of charged hypermultiplets and non-Abelian gauge bosons are elliptic parameters. To understand this structure, we show that specific auto-equivalences act on the category of topological B-branes on these geometries and generate an action of $Gamma_1(N)$ on the stringy Kahler moduli space. We argue that these actions can always be expressed in terms of the generic Seidel-Thomas twist with respect to the 6-brane together with shifts of the B-field and are thus monodromies. This implies the elliptic transformation law that is satisfied by the generating functions. We use Higgs transitions in F-theory to extend the ansatz for the modular bootstrap to genus one fibrations with $N$-sections and boundary conditions fix the all genus generating functions for small base degrees completely. This allows us to study in depth a wide range of new, non-perturbative theories, which are Type II theory duals to the CHL $mathbb{Z}_N$ orbifolds of the heterotic string on $K3times T_2$. In particular, we compare the BPS degeneracies in the large base limit to the perturbative heterotic one-loop amplitude with $R_+^2 F_+^{2g-2}$ insertions for many new Type II geometries. In the rigid limit we can refine the ansatz and obtain the elliptic genus of superconformal theories in 5d.
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