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Be careful about hardlinks. They do not make a copy. Instead the same physical file now has two names. If you open one name and change the file then the other sees the changes. If instead one name is deleted and then readded then the link is broken and you now have two copies.
The issue here is metadata.db. Hardlinks won't be broken when calibre opens and writes one of the names.
If I misunderstood what you are saying, sorry about the spam.
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