I understand this as a security feature and important behavior by design. of course it’s not nice to loose the Zymkey together with the Pi, but it also makes sense. Nobody can steal your device, move the Zymkey to another board and try to break some security and encryption. Also no other “productive” Zymkey will work with your device.
May see it in this way: just because your i stopped working the RAM and USB-Ports probably are still functioning. But you will throw it away because the board is dead. By pairing your Zymkey to this board, you virtually “soldered” it on this board.
Not sure if this helps, or makes you feel less sad. It is the way how it was designed and how it should be.