If a user makes changes to an application configuration, are those changes written to the virtual layer?

Chris asked, "If a user makes changes to an application configuration, are those changes written to the virtual layer?"

Yes, Chris, by default those changes are saved to the writeable sublayer of the VSP. So when the application is reset, those changes are discarded. If there are things that you do not want lost in a reset, you may use either excludes (which saves specified items to the base) or data layers (which saves specified items to a separate layer that is unaffected by a reset).