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If I get this right you're basically trying to create a classification system, but you need to add to it on a continuing basis. I don't think that you really want to go down the route of a numbering system at all. It's going to get super unweildy and end up like a library, with the dewey decimal system, only librarians really understand it.
Personally I'd use something like a taxonomy diagram:
You get several benefits:
it's really expandable
You can call the books whatever you like, it won't matter
it's really easy to see where you should start without a complicated numbering system.
In hardcopies you only need to add the relevant section, fans will be able to understand exactly where the book fits by looking at an extract of it.
For the softcopy (which you've mentioned you want to move to), they can see the whole system at once and you can auto-update when a new item enters the canon.
The downside is that it can get unweildy but since you only need an extract to understand where that book fits that isn't really a problem.
I genuinely think that for ease of use by fans (especially new ones) any form of numbering system is a bad idea. A diagram is the simplest option.
It also means you can cross link stories. Take Title Fight, it happens between The Starter and The Rookie but is referenced in The Starter. If you're universe expands as much as you plan that sort of instant reference note is going to come in really handy.
You'll also have the ability to customise it with labels for different themes of content (e.g. football, military, politics) or nature of product (ebook only, videogame, hardcover only, audio only...)