Updating over BLE is not the safest method. If it fails, the device is left with the bootloader only, no application and no BLE for updating.
That it fails in the Arduino version of nRF Tool app is because nRF changed something in their Android nRF Tool app. This forced us to update the bootloader. Updated bootloader is available in our WisBlock repo. Discussed in RAK 4631 over the air update
For the problem that the devices are not responsive after updating, you say the devices are flashing the green LED. If the bootloader is working and the device is in bootloader mode, it would be more a dimming on/off of the green LED.
A fast flashing LED is showing when the device is still in upload mode. Do you get the same when you complete power cycle the devices?
If nothing helps, try to flash the bootloader, softdevice and an application as shown in this tutorial.
The files are in our Download Center
Flash in this sequence:
(1) rak4631_factory_bootloader.zip
(2) rak4631_factory_softdevice.zip
(3) rak4631_factory_application.zip