It seems editing no Main Story related quests like the Giant, the Mermaid, Shino, etc, doesn't matter much but anything related to main characters like Reika, Keigo, Takumi, Sally, etc and the bosses/stones (and other collectibles) can fuck up progress and result in doubled up NPCs.yea i did mention that before...well main quest doesn't work with editing progress..it will broke ur save
If nothing else with the extra story npcs in theory I think you can just delete the from the save, but, as I'm finding out just adding/ removing character data from a save doesn't necessarily work that easy
We desperately need a save file editor or something lol