Ok right off the bat after like 2 days the entire scene where i meet the boss again happens. i don't know if that was in your developer log for the paths save being loss and this is why or is it just a bug. but i'm meeting the boss for the second time but the game is treating it as the first time. even after i just went to the school and talked to the principal and Stacy about the boss.
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That's intended. There was a bug in the previous version where the boss shared the same code as another event making it possible to lock you out of lots of stuff. The only solution was to either have the boss show up again or to break the save files of many players forcing them to restart. So I chose the first option. What's also known is that the load slots are bigger since your old save file remembers big thumbnails from your old save files.
Anyway, stuff like that sometimes happens when developing/revamping things like the interface or code it's a minor inconvenience for returning players while for others it's a great solution. We did lots of playtesting so there should be no other issues.
Cheers!