Yeah, the only thing you really have to worry about is how a little bit of Yuguri text goes, if you're already whatever her race is. It's not really retconing anything. Maybe people make note that you're a rare race, maybe not.
The Rouges' guild isn't a retcon either. It has really been there all along. Just as if you had never noticed the Lancer guild had existed, you wouldn't have been a lancer, you didn't know the rouges guild until now. You just had a little help maintaining your ignorance for so long.
I imagine you'll have to start from one of the original city states. Perhaps there'll be new base classes you can pick, maybe not.
But I can also see them pulling a kind of 2.0 transition. Since it's 3.0 and they have a continuous story to tell, new characters from new starter-villes might just start on the new story! Old ones can easily be transitioned in.