How can I obtain the X window handle of an embedded window or control?

I have created a program that I embed an Emacs instance in, similar to - https://stackoverflow.com/questions/17982831/emacs-embedded-in-a-qt-application . As can be seen there when the parent window changes the Emacs window doesn't change. I want to use a tool like xdotool to resize the window, but xdotool does not return the handle of the embedded emacs, but the one of the application window it is embedded in. Even Emacs's own command to return the handle returns the handle of the embedding window, not its own handle. I can only assume that the tools for querying the system for the windows don't see the embedded window as a Window. I suspect that instead of running in a window, the Emacs instance is running in a control and an utility that can list the controls rather than Windows is what need.