When I go to reload a room that uses physics, the game crashes, due to the physics no longer being enabled after reload, which causes errors in physics-based objects or basically anywhere where I use physics-related code like phy_position_x/y or phy_active. When I look in the debugger, before the reload, room_get_info(room).physicsWorld is true. After the reload, it is false. I don't get a crash IF I destroy all physics-using objects, which is impractical. Not sure if the fixtures of those objects are also being lost. 

I need to be able to use this tool to massively speed up my level design process, but my player character and many objects use physics, so it makes it virtually impossible unless I destroy those objects first, which messes with the overall design process. I don't manually set or bind fixtures, I just use the built-in collision shape editor with physics enabled on those objects, and physics enabled in the room. 

You could tick the “use physics” checkbox in your template room, though as far as I can tell, GMLive should be calling physics_world_create and co during room setup if the room had it checked - if you can reproduce this in an empty project, email me a sample.