Took a chance and reflashed the ZWave chip using the script below; the "1" flag means stand alone. I don't recommend doing this unless you are desperate. The script stops the LUUP engine, works out what ZWave firmware to use and then zaps it to the ZWave chip. ZWave LED then stayed on, as it should.
The log of what happened can be found here:
Rebooted and logged in via the UI. Went to the list of backups maintained by MCV and backed up from a known good one, with the ZWave check box, checked.
Once that was done - can take some time on big systems eg 30 minutes or more - waited a bit, rebooted and refreshed the browser and everything worked again.
This all started due to lack of space on Vera 3 when upgrading:http://forum.micasaverde.com/index.php/topic,38928.msg317351.html#msg317351