I'm not sure I fully understand, so apologies if this misses the mark.
I've faced (I think) a similar problem, where there's a many:many relationship between content and the documents it needs to be presented in. For example, a 'project overview' that needs to be included in a requirements document, project plan, etc.
Thus far the best solution I've found is:
- Write each section in Markdown format. There are some nice editors that make writing Markdown easy and efficient (e.g. Mou on OSX).
- Use Pandoc to convert Markdown into Restructured Text (RST).
- Use Sphinx to generate documents from the RST files.
I have multiple Sphinx doc templates, each of which combines some of the common sections with others specific to that doc. If one of the common sections gets updated it's easy to re-generate all docs to incorporate. Version Control is pretty straightforward as the source files are all simple text. Sphinx can also generate multiple formats easily: for example html to put online, or pdf for printing/distribution.
You could remove the need for step 2 by writing in RST natively. For me the extra step is worth it as I haven't found an RST editor that's as comfortable or efficient as Mou. YMMV of course.
It's not a perfect solution: for example, creating links across sections isn't that easy. But in general it works well for my needs.
hth.