Modifying a model breaks connections

I found some related issues, but very old from 2011, so I'm raising this issue here to find out what's the current situation and if there are any workarounds.

We export 3D models in FBX format, and use them within Unity. We do some mix & match of models, so for example we instantiate hair, beard, and weapons, in-game, under specific parts of the model.

The problem is, every time we do any change to the FBX file, everything stops working: the model in the prefab is no longer linked to the new model, so we need to remove the old one and add a new one, requiring us to set all the placeholders again...

Is there any way to update a model without it breaking prefabs that use it?