Thanks for the reply :)
Unfortunately, even in 'safe mode', Line6 Monkey (v1.73) shows the flash memory in an unknown state. Because of this, the 'update selection' button is greyed out also.
If I connect over MIDI, I am able to update the flash, but so far no change in the display/behaviour… which makes me think that the flash isn't actually being updated! My MIDI interface shows messages being sent from the computer to the PodXT, but nothing on the return channel (I would kind of expect some kind of acknowledgement from the Pod, but that might not be the way the reprogramming works!)