Re: How did the Nero, his crew and ship escape Rura Penthe?
Perhaps Nero wears a prosthesis that itches, so he frequently removes it? Thus, any "early" scene of him showing an intact ear fails to be proof of his ear being intact "back then".
I heard from someone that there's a deleted scene where Ayel comes in to give Nero a report partway through the movie, and the camera cuts to Nero's back, and we see the prosthetic ear being lowered onto his head before he turns and asks Ayel to give his report.
"You have been examined. Your ship must be destroyed. We make assumption you have a deity, or deities, or some such beliefs which comfort you. We therefore grant you ten Earth time periods known as minutes to make preparations."