Is there any harm in advance VAG programming to for the rns-e even if there is not one actually connected? In other words, if I end up removing the rns-e and replacing the stock symphony II, do I need to "deprogram" to default settings?
Most of the settings apply only to the RNS-E, all those in STG 37 or 56. You may get an error from STG 17, your instrument cluster, if coded for navigation which is not actually present. Other than that there should be no negative effects. Howver, if you get an RNS-E you don't know the config of, it's better to check the settings after installing it.