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Generally speaking, don't touch the Calibre library. It expects certain files to be there for certain reasons, and any interaction should go through the GUI or Calibre's command line tools. The OPF file exists because of a recently added feature that backs up metadata for each book in the books directory, creating the metadata.opf file. The intention is to be able to rebuild the library database, should it be damaged, from the libraries backed up metadata.opf files.
But seriously, don't mess with the files directly. You'll be entering, as they say, a world of hurt.
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