In this paper, we consider the linear stability of ion-irradiated thin films where the typical no-penetration boundary condition has been relaxed to a phasechange or mass-conservation boundary condition. This results in the modification of the bulk velocity field by the density jump across the amorphous-crystalline interface as new material enters the film and instantaneously changes volume. In other physical systems, phase change at a moving boundary is known to affect linear stability, but such an effect has not yet been considered in the context of continuum models of ion-induced nanopatterning. We also determine simple closed-form expressions for the amorphous-crystalline interface in terms of the free interface, appealing directly to the physics of the collision cascade, which was recently shown to strongly modify the critical angle at which pattern formation is predicted to begin on an irradiated target. We find that phasechange at the amorphous-crystalline boundary imparts a strong ion-, targetand energy-dependence and, alongside a precise description of the interfacial geometry, may contribute to a unified, predictive, continuum-type model of ioninduced nanopatterning valid across a wide range of systems. In particular, we consider argon-irradiated silicon, where the presence of phase-change at the amorphous-crystalline interface appears to predict an experimentally-observed, strong suppression of pattern formation near 1.2keV for that system.