As Di0 says create a primitive navcut type box on top of the navmesh and enable/disable via script whenever you want your NPC's to be able to walk over it or not. You can also make your structure a parent object and the primitive a linked child object so whenever your structure is enabled/disabled so will the navcut box too.
Have a look at the player homes its basically how purchased house upgrades work the purchase script enables an invisible xmarker and all the linked child objects (the previously disabled and invisible house upgrade objects) all become enabled and visible too. In the case of Hearthfires theres a few navcut boxes that are disabled/enabled too where the child bedrooms will be especially Proudspire as you don't want NPC's trying to wander into a room that doesn't exist/hasn't been purchased yet.