Well, the way we have it set up is that instead of actually making an effect happen (say, incrementing a "character points" variable whenever you choose a character), we just store all the choices you ever make in the entire game. So if we want to make an early prologue choice meaningful in the future, we can do that in future builds without worry.
So like setting flags (bools) in C# that get marked true false etc for each decision and having events check for specific flags later.
Or something of the like I am just guessing cause I only know aspects of C#, or adding every decision to a list and having the game parse the list! I dunno I'm just making silly guesses at this point.