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On a case insensitive filesystem if you change the case of a title or author a mismatch between the stored ath and the on filesystem path can easily develop (remeber that author folders are shared between multiple books). Then when you moce the library blindly to a case sensitive filesystem...poof.
calibre is developed on linux which has case sensitive filesystems, it most definitely does not have any problems with using either a case sesnitive or a case insensitive filesystem in alone.
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