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One strategy is to use a different program, such as a database, to write the edits as InDesign tagged text files to both the novel and derivative files when updates occur. Hard to tell what the workflow is and why it must be done as you describe.
I think you should tell us what your real goal is. Does this relate to translation? Foreign languages? Can you give us a concrete example. It sounds like you're going about this the wrong way, though it's hard to know what to suggest instead (layers?).
I work for a small textbook company (very limited budget). They publish a core set of textbooks and they also do custom and derivative textbooks based on the core set. In the derivative sets the relationship to the core is that they are essentially just shortened version, certain chapters have been ommited. The custom is a whole other sticky mess, everything from translation to unit differences and regional spellings (US to Canadian being the bulk).
So the core textbooks are the only ones directly edited. The rest are retooled versions of the core. My goal is to find a way to automatically extend all relevant text from core to customs and derivatives.
Thanks for your future and past efforts to understand!
I can see why John asked you about translation, because what you are describing is a pretty normal thing when you're managing documents across 20 languages. "Managing" is the key word here; SDL has all kinds of "content management tools" that will make your job very easy. Unfortunately, such tools are very expensive, so they're more likely to be useful to you if you're asking on behalf of 10-30 people. But it sounds like it's just you, to be honest, so I'm not going to go into descriptions of the global-team-cat-herding tools unless you ask. (They're great, especially if you have to herd cats.)
What I do, when I'm in your shoes, is I make a "fake" translation memory. I'd align my "parent" document against itself, saying that the source language was en_US and the target was en_NZ. I'd do this because translation memory tools excel at doing what you're trying to do (reuse identical content outside of its original context, automagically, with no laborious control-c alt-tab control-v work). Of course, that's why SDL, a company that has built its fortunes on translation memory tools, has expanded its toolset to encompass monolingual content management. There are other such tools out there, of course, but I mention SDL because if translation is involved in your workflow there's a chance that you already have Trados. All that would do for you, if you were to make a fake TM as I describe above, would be to get your "master content" out of ID and into a database, which is where it belongs if you want to attempt contact management on this scale. That could be a homebrew database, or you could pick out a content management tool that was able to trigger the script to regenerate your stuff in InDesign. I can't suggest anything because I always ignore content management tools that do not have multilingual content management, localization, and internationalization built in from the very beginning.
So, homebrew: I dunno what your background in databases is like. Because I have had this conversation with Mac-based designers dozens of times over the years, this is where I usually mention Filemaker. What's your expertise level here? Because, honestly, if you wanted to script something but know nothing about databases, then I'd say: Move all of your content into Excel. Seriously. Save out CSV from there and route it into InDesign via Data Merge. Manage content in Excel. Make people submit changes in Excel. Handle change tracking by writing VBA scripts to do change tracking in Excel.
There are many other ways to do this on a roll-your-own basis, of course - I set up a little SQL database, my client set up a little web-form for new submissions, and then we collaborated on getting the database to spit out a nicely tagged XML file, which we could then import into ID and auto-magically format. This workflow is usually really thorny, but because we controlled how the XML was tagged up, it went off without a hitch. Most XML-into-ID projects are not nearly so smooth, or so I've heard. But I've never needed to lift a finger to fix the XML, it's always been perfect, and I'm told by many that usually XML projects in ID require a bunch of XSL transformations to make data useable at all. But, once again, if you have the skills and tools, this is another DIY-content-management technique worth investigating. (But pay attention if John posts about XML->InDesign projects; his experiences have apparently been as frustrating as mine have been easy.)
TL;DR: Don't try to manage your content in InDesign. Get it out of your page layout tool into a container that makes sense, like a CMS, or a homebrew Filemaker database, or even Excel. <shudder>
Thanks for all the feedback!
My feeling from the get go has been content management on InDesign is ridiculous so it's nice to get some confirmation. I don't have much experience with databases but I've got some skill in Excel. I've looked at the XML in Excel and tracking changes would seem doable in the short-term while I pick-up some database knowledge, it seems like the intersection for a lot of larger scale solutions.
Again thank-you for your time and attention, this helps a great deal.