So, if I do, say Rio's story, and then I finish it. After that I do Ayan's story, I finish that too. Well, what if while doing Rio's story I wanted to evolve Rio's Phanphy into Donphan, and get it to 100% link, as it is the perfect link, and so I upgraded all the kingdoms to pass time? Would it still be that way when I do the story again?
Well like Machalite said
1. All kingdoms revert to lowest facalities when you start a new chapter including replaying ones you already finished
2.link % resets to a low link % however evolved Pokemon hope I helped P.S. All credit goes to Machalite