How to approach dev'ing VN with weird Story Mechanic

[illuminate001]

I have an idea for a VN with an interesting story mechanic, but I wanted to find out how possible it is technically and also how difficult.

The idea: there's a main story/character and 2 sub-characters. When you finish the main story, you may play the story of the 2 sub-characters.

- Is this mechanic possible and how would you recommend this be set up?

The trick is, depending on how you played the main story...events in the 2 sub-characters stories would change. So the game would have to remember those choices made even after the game is shut down, but also be tied to the saves.

- How would you approach setting this up and are there any pitfalls you can see straight off the bat?

Obviously there's already some complications. What happens if you finish MainStory, then Save onto Save.1. You get halfway through a Sub-Story and Save onto Save.2. Then replay MainStory and make different choices but load Save.2? I'm guessing you'd have to limit the player from replaying MainStory until they play both Sub-Stories...or, the entire game can only have 1 state of "being" and if you want to change the outcome of the Sub-Stories, you'd have to delete the entire game and reinstall it fresh?

I'm confused as to how this would all work obviously.