Do these scrolls apply only to the present incarnation of the universe or are they imported into every new universe?
This is a really difficult question to answer. I've written a long reply three times and I keep erasing it. I'll need more information on what brings this question in the first place.
I believe the whole infinite universe rebirth concept was introduced in your last post by Brother Silas: "All ends and restarts in the fire of change. From the ashes of the conflagration rises a new universe. But nothing is predetermined. It’s a process of either purification, or corruption. Grace or ruin may bloom."
Unless I'm misreading, this means that the current situation in our story has repeated in other incarnations of the universe, and that the outcome is different each time. As you say nothing is predetermined.
The problem here is: I've written every spirit with the idea in mind that the universe they created is their only one. There was nothing in the beginning, and then they created everything. They had never created anything before. That's why I'm a bit stumbled. This basically contradicts the way I've been thinking this whole time.
Not that there is anything wrong with what you're asking. It just adds a whole other dimension to the story and raises lots of other questions about the spirits in particular. I tried to address them in my previous attempts at writing a reply, but things always got complicated quickly and I could never quite formulate something sound.
I'm not saying that we should remove this. If it's important to you, we should keep it. But I think the simplest way is this: The spirits don't remember each reincarnation. So, while they think it's their only time creating everything, it isn't. If we go with that, then the answer to what you are asking is: they only apply to the present universe.