I believe the logic is that there’s no session data (thus no data to destroy) if the node never joined before, so there’s no option to reactivate the device under such circumstances. That button is not about clearing data related to the LoRa gateway, but the session data (e.g. frame counters, MAC command states) maintained for communicating with the node.
If you were looking at the LoRaWAN frames view for the LoRa gateway, you can see frames appearing from every LoRaWAN node in range - even from nodes that do not belong to you. But if you saw frames in the LoRaWAN frames view for the node itself, then the messages there do indeed belong to your node.
Before concluding that the RAK5146 is faulty, have you attempted eliminating the problem through substitution? Like replacing the RPi’s power supply, microSD card, replacing the HAT if you got another board, rolling back to the earlier version of Chirpstack Gateway OS (if that worked before). I suppose the RAK5146 is one of the more expensive components in your system.
I have used the RAK5146, but not with the RPi and also not with the Chirpstack Gateway OS. It’s a mini PCIe board format, so you must be using some adaptor to connect it to the RPi. The RAK5146 would be connected through either SPI or USB (likely as a USB to SPI adaptor), which are external busses - which I think should be less likely to cause a computer to hang. Rather, I think it is more likely for it to just not operate properly.
As for location, the LoRa gateway may optionally have a GPS. The RAK5146 does, but you need to have the GPS antenna connected to it. The interface for GPS feature of the RAK5146 must also be connected to your RPi and the packet forwarder (Chirpstack Gateway OS in your case) must be configured to use the GPS. I have never used the Chirpstack Gateway OS before so I cannot advise you on what to check, but the path to the NMEA device (some serial port or a device named “/dev/nmea”) could be configured for the standard Semtech packet forwarders (e.g. UDP packet forwarder or the Semtech BasicStation).
It is possible to cat the GPS device (e.g. cat /dev/nmea or which serial port it appears as), to see whether the NMEA messages appear. From the NMEA messages appearing, it is possible to tell whether the GPS can get a fix or not (e.g. from xxRMC). The GPS getting a fix, depends on whether the GPS antenna has a line of sight with your sky.
Since you seem to have seen it work before, it must be supported on the hardware level of what you are using.
For me, my RAK5146 was plugged into a mini PCIe slot of an industrial PC. But because there’s no support for the pins where the GPS is connected to (in the mini PCIe), I could never use it.
Good luck!