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If you keep re-adding books trying to correct a minor problem ( or just using the stores app folder every time, you will frequently get dups.
There are settings that will help reduce the chance, but not a cure for a poor work flow. Fixing metadata in the Library will confuse the dup check (they are now different)
Find Duplicates Plugin, can help... BUT it should not be used blindly (false positives for many valid reasons).
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