Adding an obstacle to block pathfinding?

I need to find a way to make a "dead-zone" on the navmesh at runtime that will be ignored during path finding. In my game the player moves around large containers that sometimes block routes the navagents could use. How do I mark the spot where the containers currently are as unpathable?

 

You have two options. Either add NavMeshAgent's with the appropriate radius to the boxes. Agent <-> agent avoidance is going to do the work for you in that case. Or you need to deactivate NavMeshAgent's while you move the agents in a scripted way around the containers.

 

Is there anyway to have navagents be a shape that isn't a capsule?

 

Unfortunately no, as far as I know.