Almost any PT edit will rattle its continuity with EU material. A radical edit like Adywan's all the moreso.

For my own prequel edits, I need to occasionally remember slight differences when I read novels. In Luceno's "Dark Lord," Bail Organa's wife takes care of Leia, since Padme had died in childbirth. Because my edit of Ep3 has her survive to raise Padme on Alderaan, that doesn't mean I can't enjoy the book. It doesn't align perfectly with my edit, but I have no problem acknowledging this as I read and enjoy it. (Just hope future episodic films don't directly reference Padme's death on the operating table.)