We analyze transitions between heterotic vacua with distinct gauge bundles using two complementary methods -the effective four-dimensional field theory and the corresponding geometry. From the viewpoint of effective field theory, such transitions occur between flat directions of the potential energy associated with heterotic stability walls. Geometrically, this branch structure corresponds to smooth deformations of the gauge bundle coupled to the chamber structure of Kähler moduli space. We demonstrate how such transitions can change important properties of the effective theory, including the gauge symmetry and the massless spectrum. Geometrically, this study is divided into deformations of the vector bundle which preserve the rank of the gauge bundle and those which change the rank. In the latter case, our results provide explicit solutions to a class of Li-Yau type deformation problems. Finally, we use the framework of stability walls and their effective theory to study Donaldson-Thomas invariants on Calabi-Yau threefolds.