I can see why so many people have recommended this game, as it's very interesting and ambitious, but I'm having a lot of trouble with the flags and save states. I'm very regularly picking up items I've already picked up after I've used them, I can't seem to properly trigger new events or clear progress when switching to new books, and a lot of weird triggers keep coming up like getting dialogue for being alone in Mia's book after going back down with Mia.
Ah, yeah, "ambitious" is definitely the word when it comes to the flags. It's odd that you're getting that level of repetition though - I suspect something's gone wrong that's caused a knock-on effect.
If you like, you can email contact@spiderlilystudios.com with the "retrace.save" file you'll find in your install directory (usually C:/Users/[your name]/AppData/retrace) and I can attempt to repair the save file for you, otherwise, judicious use of "New Game" and the fast forward function may be in order. I'm really sorry about this! It's been a year and a half since release and I'm still finding new ways the variables can interact to break everything. Even so, I'm glad you're finding it interesting!