Well after that, I just had a brown trouser moment (well, several moments actually), upgrading my second battery. Went through the process and eventually after several minutes I got a long continuous tone. The centre two lights were on on the battery. It wouldn't switch off, so I pulled it. It still wouldn't switch off, but eventually it did, but then no lights when the button was pressed. Bugger I thought, it's bricked! I put it back in the Phantom and the Phantom powered up with no lights or without pressing anything. It started bleeping and then eventually it alternated between one and two lights on the battery. At one point all four led's on the Phantom turned red, but as it was still bleeping D-D-D-D I left it. After a good fifteen minutes I got all lights back on the battery and a successful tone from the Phantom. Phew!
A check of the log shows success and the detailed log showed that the battery firmware upgrade failed several times before succeeding.
Scary!