How are you versioning?
The way we do this is Conditional Text.
If the pages layouts are the same, you can generate any number of different books from the same set of component files.
If the page layouts differ, create two books, but import the Flow A for each major component file into the clone books.
IX makers and IX gen are automatic, once set up.
If the files are physically different between the books, then you'll have to add the appropriate index markers to the other files. Otherwise, if you're using conditionals on single-source files, then, as Error mentions, it's pretty much automatic.
That helps! Thanks!