I know this question is about PyPDF2, but as the maintainer himself informs it is deprecated, and this post still shows up when searching for cloning files with pypdf...

Here's how you do it in pypdf:

from pypdf import PdfReader, PdfWriter

writer = PdfWriter()
writer.clone_document_from_reader(PdfReader("input.pdf"))
with open("output.pdf", "wb") as f:
    writer.write(f)

Much easier nowadays, isn't it?