To be more specific, I'm missing Bad End 2. And my previously-acquired notes were unlocked from the get-go for this new download, but to be sure, I sped through all of Meenah's routes too. Then I ran through all the options with Aranea again but I didn't notice any changes.
I don't want to go into too much detail here in the comments but I have compiled a guide in our Google Doc that you can check out for more explicit details (spoiler warning, obviously).
Sorry it took so long to look here and get back to this, but in the end I suppose that was only to my own detriment, lol. I appreciate the guide and that you couldn't get too detailed. Turns out I didn't notice the thing was clickable because I thought it was a truck or something in the scenery. The secret clickables! Thanks, and have a great holiday