Sorry, I deleted all my saves and persistent files and started the game again. Currently working on the theory that the persistent file in the hidden AppRoaming folder (PC) that was left over from the previous version could be causing the issue (although it hadn't ever done so before), so I'm replaying the game from a clean slate to see if that does the trick.
I just started to play the game, only to find out that I am in the same boat. I only did the intro story (Annie, Headmaster, locker, gym teacher, bissette), met Erik outside school, Diane garden intro and first part of Eve's story (meet in park, do rap battle), made some mony in Diane's garden, and slept some times. Now I started again and loaded the save, only to find out that the Intro story has reset and I must get dressed for gym class again, only that I cannot do that and I cannot leave the locker room again because... you name it.
I had a save immediately after the intro, when I load that up again I am able to complete the story up to when I first leave school and meet Erik, and I can proceed normally. When I load the earlier save from exact the same point of time in game, I run into the bug described above. When I load the new save, everything is fine. I did exactly the same thing.
If the game is resetting story lines, it is truely fucked up, as much as I like it...