what you can do when the layout load, disable the solid behaviors of the objects enemies can go through, then regenerate the pathfinding obstacle map, and finally re-enable the solid behaviors. I have not tested it, so I can't guaranty what will happen when the enemy hit the doors, will they get blocked or go through? I'm not sure the collisions are tested during pathfinding moves.
Edit: in fact you can disable the solid behavior from the beginning and only enable them when layout start, the obstacle map should already be generated, this will save you from having to regenerate it