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I used to have those kinds of problems when changing metadata on a library shared (via Dropbox) between two computers -- one of which had a case-sensitive file system. Changing the cases of metadata on the the case insensitive machine would result in titles without books or weird duplicates (one with books and one without) on the case sensitive machine when running a library check.
If you must share ... do so between machines of the same platform. Or at the very least ... only edit metadata on the machine that has a case sensitive file system.
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