It looks like when using UsdImagingPiPrototypePropagatingSceneIndex, pointinstancer prototypes now live under the original prototype location (whereas previously they lived under the pointinstancer). I assume as a result, they now inherit invisibility from a parent scope.
Concretely, when not using the Stage Scene Index pipeline, the following USD snippet results in a visible instance of the sphere; when using the new pipeline the instance is invisible.