You could try removing the dongles one at a time to see if you can get it to reload the software. I'd start with the 1090 dongle.
Well, that seems to have done the trick!
All now up and running again.
One thing worth pointing out - I made things more difficult for myself by renaming the spare SD cards I was using to PILOTAWARE1 and PILOTAWARE2 to help distinguish between the two. The box doesn't like this - reformatting and reinstalling on the original card, named RECOVERY, was what the box wanted to see.
Thanks to all for the help.