If Flight Mode works via BLE the BLE connection to the lock should also work without, you just have to wait longer until the App gives up and falls back to BLE (>~10s)
You can try the compatibility mode or play around with expert settings as described in the FAQ: Smart Lock WiFi/Thread/MQTT connection troubleshooting / FAQ - #8 by Stefan_Reiterer
For individual support please contact the Nuki customer support, as this is not a support forum.