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I make one GameSession gameobject a singleton. If there is already one GameSession exists, anytime(when new scenes are loaded) a new one is instantiated,  it will destroy itself. Put timer and other persistant data in the GameSession, then it will work. 

If I didn't explain clearly, feel free to ask me.

I will try your game :)

You may want to try DontDestroyOnLoad() 

Thank you that helped :)