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Yep, it looks like PeterT is correct. I likely did an incorrect eject recently because I was following Ken's nice tutorial to get KOreader installed, there are a number of eject/power steps there and I likely screwed up one of them.
Anyways, I just connected the device to my machine, mounted the partition, and touched all the files (using linux 'touch' command which simply updates the file timestamps), and then ejected properly and then the reader did a rescan and found the books.
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