Hello
Sure you know about this, but It looks like there's a separate thread for the same issue:
https://forums.obsidian.net/topic/101706-bug-replaying-maps-cant-change-party-members-from-the-rooster/
Can't remember if I explored the Old City, but I do know I ran into some places I'd cleared showing as unexplored. I also had some conversations reset as if they had never happened, and, for example, the imp bounty NPC target reappeared even though I had previously killed him.