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How are you finding that the database is corrupted?
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There are three ways to know it:
1. Calibre pops communication error dialog in file transfer.
2. Like johnnyb has said, nickel home tiles don't responsive to modification.
3. Random books in nickel home/shelves/library having blank cover and a "buy" drop down menu on the right-hand side.
Is it possible for Koreader to broke some presumptions needed by nickel and other background processes?