Whenever a configuration is modified, the UniFi controller will detect the change and begin provisioning the affected device, or the whole site depending on the configurations affected. This is true if changes are made on the controller. However, if you are changing configurations by modifying the config.properties file, the controller will not detect the change and you will have to manually instruct it to begin a provision. All you need to do is change something in the Controller to set this in motion. One way to do this is to toggle the SNMP. To do so:
Go to Settings > Site and check the box for Enable SNMP, then Apply Changes.