That's 100% possible.
Right now whenever an NPC is supposed to spawn the game does some quick checks to see if they're supposed to be there, if you're ever in the library on weekends for example, Twilight will not appear.
So it would be easy enough to also have it check if your s-link is at a certain level, and remove her accordingly.
Opening a new area is also just fine.
The only part of this represents any challenge at all on my end is building an inbox for the player to receive messages on, but that's no real heavy workload. Feel free to write it, I'll work on incorporating it