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This is just anecdotal info but when I installed/reinstalled KOReader a few years ago, within a day or so I invariably got a corrupted database after connecting to calibre. This may have been because I didn't load the PDFs in a hidden directory so Nickel was also able to 'see' them.
Once I uninstalled KOReader for the final time I've never had a corrupted database since. But maybe things have improved since then.
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