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You can't store Calibre files on the NAS for a running Calibre unless Calibre is running on the NAS. You'll eventually corrupt the database.
The Calibre file structure only exists because putting ebooks or pdfs inside an SQL database isn't sane. Pretend they don't exist. You can't change how Calibre organises its internal copies of files.
Short answer is No, and only use the NAS to backup.
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