SOTI can handle a Zebra OSUpdate fairly well but I am not sure if the settings you are looking for will be persistent after the upgrade. You may possibly have to reconfigure wifi and re-enroll the devices with MobiControl Stage after the update is complete.
I have successfully performed upgrades from M->N (TC51, TC70x) that preserved the device configurations including wifi and SOTI enrollment, but if I recall correctly the upgrade from K->L on TC8000s ended up wiping the device completely.
Its possible that the MX Persist Manager configurations could be leveraged in order for the wireless configurations to survive the update, but I'm not sure, you would need to validate that. I'm not even sure if the older MX versions on a JB MC40 even supports Persist Manager.