Hi,
AirWave will have a reference Config and compare it with the Controller existing config. it will notify all the differences. If the device is on the management mode and if you allow, AirWave will over write the controller config with the reference config hence you will loose some of the settings.
to avoid this, wither you have allow the controller to use the local config or you have to download the controller config to AirWave so that both will have the same config.
hope you got more clarity on this.