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After a few tries (communication failures, sqlitebrowser crashes, device resetting to "welcome to Kobo" status, etc.) I think I managed to do it.
Checking cover directories, I found a few *.parsed file that should not be there (the books had been moved to the SD card). It looks like the device (or calibre) didn't remove them automatically, and the common feature I see is all of them have an apostrophe in the filename. Of course, an apostrope or quote is probably more dangerous than spaces in filenames, so I wonder:
a. Why doesn't calibre avoid them?
b. Was I just unlucky or is this maybe a sign of a bug in the firmwar (3.5.0) or in calibre?
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