Why indeed? That's what I asked myself when I came across that behavior in Ren'py. When you load a save in a newer version of a Ren'py game, any new variables added in that version are apparently added at exactly the point where you loaded. If you perform a rollback before that point, the changes made to variables in the update disappear as if they were never there, which, as far as Ren'py is concerned, they never were. A lot of players ran into bug after bug after bug in the early versions of LLtP because of this, and it didn't stop until I set a limit to rollbacks to prevent them from going before the latest save you loaded.