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@jangell2: CM's import will *never* delete a collection, so, if you ran the import after each tweak, that would explain the book in two collections thing.
As for the the other one, the exact metadata involved would help pinpoint the issue. But I'd expect it's the same kind of thing than the first one, a remnant of the first bogus sync, and since CM never deletes collections, you've just noticed the stray 'broken' one.
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