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Originally Posted by GavinZac
The only thing I can think of so, is that perhaps it tried to update metadata, thought it had succeeded but it hadn't. Again, is there a log file I could go through?
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That would at worst have removed a single folder, not all of them.
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The folder is there, the metadata.db file is there, and one other folder, a folder called "Nora Roberts" (don't laugh, it's my girlfriend's honest  ) with absolutely nothing in it 
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I really can't think of a situation that would lead to this, and I've never heard of it happening before. What linux filesystem is your database stored on?
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Is there a way to check if there's anything in the metadata.db file? I've assumed its empty because Calibre doesn't show anything, but I could be wrong.
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The database is a sqlite database. You should be able to use any of a dozen different tools to browse the database.
Best way to get a log is to simply start calibre in a terminal. It will print any unhandled errros to stdout (it also shows them in the GUI).