Hi,
you should use the method Save Instrument after you change the default values. The problem is that you can't use it on an existing vi when you have opened a reference on, it returns an error.
A workaround is to move first the vi to a temporary location, open a reference on it, change its default values and save it to the target destination. You don't need to open the front panel.
See attached image for saving vi.
Good luck,
Alberto