I've been co-using nickel, KSM, and koreader for quite some time, and I've never seen database corruption that I would atttribute to anything other than nickel or user error. And I only use the dotted directory trick for PDFs.
I've seen nickel database corruption from:
- malformatted books nickel can't process properly
- unclean USB unmounts
- copying books straight to the SDcard, rather than doing it through calibre
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