Yes, you can get a reference to the RadPane client object that is in the child page of the RadWindow control. In order to do this, you should define a function that returns a reference to the pane object on the page, opened in the window and then call it from the parent page the following way:
contentFrame = $find(
"<%= RadWindow1.ClientID %>"
pane = contentFrame.contentWindow.GetRadPane();
I have attached two simple pages that demonstrate the approach.
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