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The easiest thing to do would be to click on the Library icon at the top of the Calibre screen and select the option to Move the library to a new folder. This will cause Calibre to move the files it know about to a new location leaving behind any files that are not part of its library.
Note that when you add books to Calibre it makes a copy of the book, leaving the original unchanged. Therefore I would expect your disk space to reduce as at this point you have 2 copies of every ebook file. It is up to you whether you want to keep the original or simply rely on the copy that is stored within Calibre and therefore delete the original (or perhaps move it to an archive so it can be kept offline).
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