User blog comment:DemonicsFire/RWBY Ships Hurt/Heal/@comment-28288412-20160811002012/@comment-28288412-20160811225238

(Sigh)

She had a soul, got chopped into bits and left in a place where it is difficult for Atlas to get her (Grimm and such, presuming the stadium didnt crash after everything happened and exploded into bits). For all intents and purposes Penny is dead.

If anything the easier choice is to make a new Penny bot, one that improves on the weaknesses of the former and one with a different appearance that most of the population won't recognise.