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Calibre does not touch your original files - when you add a book file to Calibre it COPIES the book file. You shoud not try and place your Calibre library at the same location as a none-calibre library or things will get very confused.
If you made the mistake of starting along this line, then he best thing to do is to use the Calibre facility for moving a calibre library to move your current calibre library to another location. If you do so, Calibre will move all the files it knows about to the new location. Whatever is left behind will be files that Calibre does not know about.
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