I've no idea how it happened, I'm afraid. I was just deleting and adding some books and it went.
I renamed the file in case there was anything of value in it, and things are OK again. Thanks for the help!
After changing a few settings on the Kobo, I saw a new file get created.
I'll keep an eye on it. It does look odd that the file can be replaced with the contents of another file so it could be Kobo's FAT code is screwy, or Apple's, or there's something underlying in the flash. Or it could be the old standby, cosmic rays :-)
Apple's Disk Utility just gave the filesystem a clean bill of health, FWIW.
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