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The problem is that calibre bases what it is in the library on the contents of the "metadata.db" file. It sounds like the one in your "Calibre Library" is the new one from the newly created library, not the one from the library that was the original one.
Check to see what other copies of this file you can find on your PC; one of those might be the original one. However, it will not contain the "new" books only the old ones from pre stupidity.
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