During the first service boot after upgrade to XCO, XCO queries the SNMP and NTP configuration on the device. These configurations persist in the database, which is managed by XCO.
Breakout interfaces and interfaces that are in admin-state down, with non-auto speed or non-default MTU values, persist in the database and are managed by XCO
If you update the configuration, use the XCO CLI, not the SLX-OS CLI on the device. This ensures that the device configuration matches the XCO configuration.