NavMesh with scripted LOD prefabs

I'm trying to make a space station, I want to instance as mush as possible, And with a working navmesh agent, I'm going to try to dynamically script the prefabs that will be the rooms,cargo bay's, etc. they are going to be scripted LOD as soon a you perform an action like opening a door etc.

I was wondering if you can bake navmesh layout, inside all the prefabs and still have a working route?

Thanks in advance,

Regards, Ronald van Erp