But it can still wreak havoc if you use hardlinks or softlinks, because maybe there was a good reason for having a duplicate file! Imagine you have a photo “foo.jpg.” You make a copy of it “foo2.jpg” You’re planning on editing that file, but right now, it’s a duplicate. At this point you run your “deduper” that turns the second file into a hardlink. Then a few days later you go and edit the file, but wait, the original “backup” file is now modified too! You lost your original.
That’s why Copy-on-write clones are completely different than hardlinks.