Yes, all you have to do is to copy the patch into the game folder. And no, future patches don't include any of the previous version contents (otherwise what's even the point in making them if they're gonna be just as big as the game?)
You will find out more about this specific path later on with Pepper starting her relationship with another person.
Reese as an active character is gone from the game. However, you will still keep seeing her in dream sequences, videos, and all that. She will also appear one more time in the ending.
Bree is a secondary route, as I state in the walkthrough
Yes, Zoey is off-limits for Blake. I originally created her as a character who's not attracted to Blake sexually, just because everyone else is. Plus, just like Reese, she's now out of the story.
This codex line is just a placeholder of sorts. Blake's identity depends on many, many factors, and getting them all together is a bit too much for me right now. Blake is a woman on the bimbo route, and on all the others he just doesn't really think about it.
Interesting. I've never seen this error before. Since it points at the codex, could you try to delete the codex folder (Shattered/game/codex) to see if it changes anything?