I may be misinterpreting your comment, but if not, I think the problem is simply a misunderstanding of link chapters.
So, if you want to have the following two routes possible:
1. A -> B -> D
2. A -> C -> D
All you need to do is the following steps:
1. Write chapter A.
2. Write chapters B and C as new chapters branching from A.
3. Write chapter D as a new chapter branching from B.
4. Add a Link Chapter to C that sends the user to chapter D (If you are unfamiliar with this process, it is as follows: create the new chapter after C and select the "Link Chapter" option in the right bar. A box will appear asking you the chapter you want to reference, and you can type chapter D's name until it appears as an autocomplete. Give the link chapter a title, usually the same as chapter D's, post the chapter and you should be good to go).
I just ran through these steps in an unposted test story and confirmed. Hope this helps.