Interestingly, this isn't an LXML bug.  It is a documented difference from how the standard library works:

    https://lxml.de/tutorial.html#elements-are-lists

So, if you want use random.shuffle(), you need the standard library ElementTree instead of lxml.

This:

    from lxml.etree import Element

    root = Element('outer')
    root.append(Element('zero'))
    root.append(Element('one'))
    root.append(Element('two'))
    root[0] = root[1]
    print([e.tag for e in root])

Produces:

   ['one', 'two']