References to model disconnect from prefabs after updating models

When I make a change to a model and re-import it into Unity all of the references to the model’s mesh and materials disappear (says “Missing(Mesh)”). This is incredibly annoying, as if I want to make a palette swap on all of my objects, I have to re-assign meshes and materials to around 40 objects, which can take over 20 minutes in a lot of cases, even for a small game. Instead of using the model prefabs directly, I’m using references to the mesh + materials, to allow me to easily change pivots.

Pictures here

Note: I’m using MagicaVoxel for models, and then importing them with the MagicaVoxel Qubicle To Unity importer from the asset store.

I’ve just done a little more research and I think I need nested prefabs, which aren’t in Unity yet :(. There is one on the asset store for anyone who desperately needs it, but 40 dollars is a bit much for me to spend when Unity is releasing this feature later this year.