Why not do both?It's not like you need to write it twice, if you plan ahead...
You could make several short ebooks. The customer can buy them individually for a cheap price, or get all of them at overall saving.
Or, you could make several short ebooks. Use different file names for the HTML pages (except index) which don't conflict.
Then copy the HTML files for all the ebooks into a new folder. Create a new index, plus any "glue" chapters. Then compile that into the "bible" version.
I understand Michael Campbell, the search engine expert guy (Nothing But Net, etc) did something like this with his search engine reports (I'm not sure whether these are still available for other unrelated reasons)