There is no SAFE, completely automated way to do this.
Find duplicates doe get false positives. That is why it offers more than 1 'dup' detector.
Nothing beats the ole' Eyeball Mk 1.
And what if they are 'almost' dups, that you want to keep BOTH? (orig edition, 2nd edition? English and French?)
Maybe if you were not in such a rush to begin, you would not be spending all this effort cleaning up?
One of the first things I did with Calibre, was document my 900+ paperback collection. It took me over a year of, a dozen at at a whack, metadata cleanup.
GIGO