Very cool! I've been playing around a bit with BEPU as well, but I haven't done anything that cool yet. I'd be curious to know how you are breaking things apart like that, as well as what you are using to handle your camera (the standard BEPU CharacterController, the simplified CharacterController, or something more homegrown?).
The main environment is just a collection of static boxes that I replace whenever a change is made. I'm using MorphableEntities for the movable objects, so instead of deleting the entity and replacing it with a new one, I can just replace the collision data. I use a home-grown algorithm to find the (hopefully) smallest number of boxes to construct each shape.
For the camera, I'm using the BEPU simple character controller, bu it's very limited. For example, if you're walking on a movable object that has a floor and a wall, and you walk into the wall, it will actually start moving the object, when it shouldn't. I'll have to replace it eventually anyway, in order to implement more parkour elements.