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I did back up the library and restored it (after turning off syncing) so I'm good now. But I'm still not sure what really happened here. I assume it's bidirectional syncing (via the cloud), but I can't think of anything I did that would cause it to delete lots of e-books. The E-books that were sent to the trash were in the excluded folders.... and strangely enough, their metadata files were still in those excluded folders, but not the source e-book.
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