I think the problem is that I used my computer to do the format and just asked it to format as a FAT32 partition. AFAIK there is no format capability on the Opus itself. I tried flashing with the new firmware, and also with the Mobi 1.5 firmware and in neither case did it recreate the files.
When I searched for info on this problem I found many posts from Cybook users lamenting that they had done a similar thing so I am not uniquely stupid ;-) It's just a shame I didn't read the rest of the instructions where it said to backup the system files first!!