I've often thought that here should be a note attached to each 'branch episode' that carries a 'what you need to know' list of details specific to that thread at that point. Things such as active character's names, constraints from past wishes, specific plot line rules etc...
That note would pop up as you added a branch and give you the need to know history at that specific node, and the author would then update it with anything important that they added in their new branch.
A kind of reference sticky that'd help authors dip in and out of different story lines at any point without worrying too much about breaking past continuity.
