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You'll have to use either an external HDD or a network share as a temp device. Then, either you move your current ebooks folder to the temp and import to a local Calibre library; or you create an empty library on the temp device, import your books there at your leisure, and when you're happy with the result you remove your local ebooks folder and move the Calibre library on your local drive.
I'd go with the first solution myself.
(There's also the painful way: import your books by 10GB-sized chunks then deleting them. I'd never have the patience myself.)
N.
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