There is a nearly continuous record of magmatism through the Late Cretaceous–early Paleogene in Idaho and adjacent areas of Oregon and Montana, including the various phases of the Idaho batholith. We suggest that much of this magmatic record, however, has been obscured by subsequent tectonic deformation, erosion, and magmatic disruption and cannibalization, the latter of which can be tracked by zircon inheritance. Specifically, a mid-Cretaceous magmatic arc was significantly deformed by the western Idaho shear zone and intruded by the 83–67 Ma Atlanta peraluminous suite of the Idaho batholith. The northern part of the Atlanta peraluminous suite was, in turn, intruded by the 65–55 Ma Bitterroot lobe of the Idaho batholith. Consequently, the present age distribution of magmatism is strongly biased toward the youngest phases of plutonism; much of the older phases were destroyed by tectonic, magmatic, and erosional processes. The destruction of granitic batholiths may characterize Cordilleran-style orogens worldwide, which can lead to significant underestimates of magmatic fluxes.