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ONLY use the Calibre MDE to change metadata in the Library (this affects the filename as well)
NEVER USE THE OS to change a name in the Library folder., as you discovered, it breaks the linkage (the book is still there. It is just Lost)
Once you set the LIBRARY metadata, then use Embed , Polish or Modify EPUB (a plugin) to force it into the book file.
Do visit the official FAQ at the Calibre Help page. Lots of things there that may save a lot of grief later.
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