For Juniper Networks EX/QFX Series Switches that are adopted into the Juniper Mist cloud, but are not managed by Mist, the downloaded configuration will not match the configuration in the switch CLI.

You want to update the configuration file in the cloud for a switch that is not managed by Mist. It is expected that both will differ.

To update the configuration downloaded from a switch that is not managed by Mist, you will need to update the GUI to reflect that of the switch CLI using the GUI or additional CLI commands.