Geez, I show up two hours late and there's 8 new pages of crazy speculation on time mechanics that we should already understand. It's not exactly "simple" but we've seen stuff like this before. How is creating a timeline where they arrived at different points different from creating a timeline in which a Dave which never existed arrives and saves John's life, except in the scale of the change?
Skaia basically exists whenever. And unless I'm reading something wrong, it's specifically stated that scratching the record and bringing it to Skaia changes where the portals went. So basically, everybody gets sent back, the scratch happens, and then everybody gets sent back to different times. It is, in my mind, exactly the same as John dying, Dave learning as much as he can, and then Dave going back and saving John.
The troll session is only a slight bit weirder. I'm not sure I fully understand it, and it's possible that all that changed is Doc Scratch was sent back instead of whatever the alpha first guardian is supposed to be, but I don't fully understand the arrival of the first guardians, because I don't know where the heck GCAT even comes from.
Here's my theory though. When Karkat sends the trolls through their portals, they initially arrive at their alpha destinations. Something happens, even though it sounds like they did fine, and they're forced to scratch the session. This scratch changes the destination of the portals they arrived through, and it creates the beta session. I can kinda see a problem with the troll alpha session causing the scratch, but it's still a basic paradox in which somebody changes the situation leading to their arrival, and since it was always going to happen that way, it doesn't affect things too much.
I'm kind of getting the impression that a beta session is one that gets to create players, and an alpha session is one that doesn't, but it's gotta be more complicated than that. However, I feel like all this talk of the scratch being a hard reset is just to hide the fact that all it does is turn the session that causes it into a doomed timeline that basically never existed. Time travelers can't get to it though, because in the new timeline, they never learned time travel to be able to get back to it. Or something like that.