In that case I’m not sure I can explain what was going on but glad to hear that it works during “normal” usage (factory resets instead of reprogramming). We fairly frequently run the test scenario described earlier where the parent of an end device is removed to force the end device to rejoin through the coordinator since this is how we verify that end devices do secure rejoins.
Could you PM me a sniffer trace showing this and also send hub logs after running the test?