Yes, it is possible to design your branching to be non-rejoining in the future. I can’t recall this being done for a major story-stream (terminology is not precise, sorry) but it is done for side missions and asides all the time. CS allows you to jump from one scene to another and even within a single scene jump to various places using labels that are unique.
I’m going to link the CoG development theory here because this will give you an idea where the publisher stands for official CoG stories. This is not something you have to follow for a Hosted title but it will give you an idea of their game making/storytelling philosophy.
Here is a thread that might also help you; the first post has a worthwhile doc to read about branching in general for IF fiction.