You can replace objects in PDF documents. A PDF is mostly just a bunch of objects of different types so the readers know what to do with them. Each object has a numbered ID. I recommend mutool for decompressing the PDF so you can read it in a text editor:

    mutool clean -d in.pdf out.pdf

If you look below you can see a Pages list (1 0 obj) that references (2 0 R) a Page (2 0 obj).

    1 0 obj
    <<
      /Type /Pages
      /Count 1
      /Kids [ 2 0 R ]
    >>
    endobj

    2 0 obj
    <<
      /Type /Page
      /Contents 5 0 R
      ...
    >>
    endobj

Rather than editing the PDFs in place, it's possible to update these objects to overwrite them by appending a new "generation" of an object. Notice the 0 has been incremented to a 1 here. This allows leaving the original PDF intact while making edits.

    1 1 obj
    <<
      /Type /Pages
      /Count 2
      /Kids [ 2 0 R 200 0 R ]
    >>
    endobj

You can have anything inside a PDF that you want really and it could be orphaned so a PDF reader never picks up on it. There's nothing to say an object needs to be referenced (oh, there's a "trailer" at the end of the PDF that says where the Root node is, so they know where to start).