It turns out Designer updates not pushing to the new window was worse than I realized at first. What happens is the original window is redrawn and the new window quits running (though it still displays everything that was there, bindings stop updating, etc).
Solution found for automating contentPane update on Designer update push: The trick is updating only the new window (not the original contentPane is grabbed from). This is accomplished by checking for a unique title assigned to the new window on creation (see code above). It is not possible to use a custom property bound to edit count to trigger the update as bindings in the new window stop updating. Instead we filter for a property change on componentRunning and then regrab the contentPane. It is necessary to use invokeLater with a bit of additional delay (using 10,000ms) for the redrawn original screen to show up as open for grabbing (otherwise get an error for window not open).
So far this update solution appears to work great with no known bad side effects.