I wiped my save file in the menu with the 3 save files, and when I went and started a new game in the save file I deleted, my pencilmarks were still there. Is this intentional?
Yes, it's a feature intended to assist in future playthroughs or speedruns. Press Ctrl+Shift+D while loaded in a savefile to delete all of that savefile's pencilmarks.
I see. That makes sense. Although maybe an option to also delete pencilmarks when deleting a save would be cool. Or just informing the player in-game about that hotkey.
