What firmware version are you running? Endpoint 3 was only released in 2.18. If you’ve updated to 2.18 and are still not seeing endpoint 3, you’ll need to reinterview the switch.
If you do it via the binding, than it will work if Home Assistant or Zigbee2MQTT is offline.
You can do it in Home Assistant by using my blueprint to capture the action of the config button in an automation: [zigbee2mqtt] Blue Series 2-1 missing action sensor in Home-Assistant - #15 by rohan