In Flair, a zone is created when a thermostat or an IR device is added. A room is then associated with the zone that controls it.
For example, adding a thermostat called "Hallway ecobee" will create a zone called "Hallway ecobee". If that thermostat controls the downstairs rooms, you'll want to make sure those rooms are associated with the "Hallway ecobee" zone.
To verify zone configuration, tap the room to view the room tile. Then tap the 3-dot menu, and select Settings->Room Info.
Confirm the room is in the correct thermostat or IR device zone (the correct box should be checked).
If using Mirror Mode, or Secondary Heat, the room must be in both the mini split zone and the thermostat zone that it is following.