It's expected behavior: every time you visit a layout, it is created in its original state in the layout editor. This is so that if you blow up some walls or something then restart the game, you don't have the same "ruined" layout.
Having said that, though, perhaps a "persist state" option for layouts would be good for Construct 2: if you enable it it saves the layout state so you can return to a layout as you left it, or use an action to explicitly reset the state to the initial state.