Model re-importing adversley effects prefabs

When re-importing models (.fbx files) into unity all prefabs linked to the model bug out… Objects on the prefab always lose their rotation and position. Currently if a model is updated and re-imported we have to re-create the entire prefab and re-link it. This can sometimes be a complex process as our prefabs may be a combination of several different models, scripts, materials etc. Not to mention in some of our scenes a prefab may be used 100s of times. It’s quite time consuming having to re-create them and then place them again in the scene.
Does anyone have any idea how we can get around having to re-create prefabs if a model is updated?

Thanks in advance.

What if you kept your models inside a container GameObject, and rotated/scaled that, so when you replace the model, you don’t lose that data?