I saw your question about stopping the 'X' from closing a Tk window, so I pulled up one of my old apps and started playing. If I add the following line after creating the window ($gMainWindow), the text "Mooo!" will be printed each time the 'X' is pressed.

$gMainWindow->protocol("WM_DELETE_WINDOW", sub{print "Mooo!\n";});

By adding this code:

$gMainWindow->protocol("WM_DELETE_WINDOW", sub{print "Mooo!\n";sleep 5;$gMainWindow->destroy;});

The text "Mooo!" is printed, the program pauses 5 seconds, then the window closes. So... using this sub, present the user with a "Yes/No" message box... if they select yes, use a $gMainWindow->destroy, otherwise continue with the program.

Does this help?