Utilizing the large N dual description of a metastable system of branes and anti-branes wrapping rigid homologous S²'s in a non-compact Calabi-Yau threefold, we study phase transitions induced by changing the positions of the S²'s. At leading order in 1/N the effective potential for this system is computed by the planar limit of an auxiliary matrix model. Beginning at the two loop correction, the degenerate vacuum energy density of the discrete confining vacua split, and a potential is generated for the axion. Changing the relative positions of the S²'s causes discrete jumps in the energetically preferred confining vacuum and can also obstruct direct brane/anti-brane annihilation processes. The branes must hop to nearby S²'s before annihilating, thus significantly increasing the lifetime of the corresponding non-supersymmetric vacua. We also speculate that misaligned metastable glueball phases may generate a repulsive inter-brane force which stabilizes the radial mode present in compact Calabi-Yau threefolds.