You do not need to create two update paths.
Assuming you have class A, which is the class you originally designed. Create a refit for class A, for example A-2. Then create a copy from that refit, for example class B, and build a few ships of that class. If you now create a refit for A-2, let's call if A-3 because we are really creative today, you can then refit ships of class B to A-3. It's still more annoying that just building A-2, but at the end of the day you can keep one upgrade path, regardless of how many refits you do and how many classes you branch off the original path.