It seems that there are troubles with navmesh realtime (i have seen some threads about that on answerhub :
https://answers.unrealengine.com/questions/39418/rotating-door-does-not-update-navmesh.html
https://answers.unrealengine.com/questions/38619/rebuild-navmesh-in-blueprint.html
But i just got an idea maybe right to help you time the trouble is solved : Creating separate navmeshes and spawn / set the ones that are ok and not the others. Like a branch : true then spawn the building. False then spawn the navmesh. (with a toggle active for example.)