That's one of the tricky things about being a dev: you already know all the lore and whatnot, but the player isn't caught up with you yet. It can be easy to lose track of things.
As a suggestion, if you don't already, try taking copious amounts of notes. Any idea you have for your game(s), write it down. Even if it's something that ends up not being used. Also, if possible, try to keep things roughly sorted by date to make it easier on yourself to find things later. That way, you're less likely to run into another "what was I thinking 7 months ago when I did this?" again. (There's pros and cons for both physical notes and digital notes.)
Lastly, maybe you could make this version of Between Two Points as a "prototype" version where you are/were trying out various ideas. That way, you can do Lyra's story how you originally intended as a "new" game while this prototype version either just exists as-is or or could maybe get irregularly updated with ideas that don't quite fit into Lyra's main/intended story.
Viewing post in Between Two Points: Taking a Step Back comments
Yeah, I've been starting to take notes since Episode 3. Tbh I haven't taken any notes during the first two episodes apart from dialogue of course. I downloaded some sticky notes for desktop and put in little things I had to do and any idea or important thing that I had to remember.
I also started using Obsidian with Canvas and created a big mind map for things like how systems, relationships, stats & stories of the girls work. Basically every scene for the main story or a scene a girl gets attached to their own branch so I have a direct overview what happened. The girls for example of the new game have stats like Trust, Affection & Intimacy (not final names), so progressing too quickly can't happen that easily.
I mean you could see this BTP version as prototype because it is a failed project in a way. Not horribly bad but also not good enough. This game side will stay online most likely anyways and the new BTP or other game will get their own page.