build and run/ saved scene is not updated when application is loaded.

I add the current scene before building the project. I had set the application.loadlevel(int); to the current scene.

But when Im on the menu and load the level the changes I made on scene was not updated. example I add a new object on the scene and when I build and run and load the level its not in the scene or in the heirarchy.

Before testing adding new test objects, I add two object with sprite render, boxCol2d and set its (sprite render)layer to HUD.. but when I save the scene add the current scene and build and run and load the level... booom and ending the two objects go to default (sprite render)layer. :(

What do you think cause this ? It's very unusual for me because this is the 1st time it happened to me and can't figure out where to fix the problem even I set it by code(supposed to be not).