Ah, I understand now. Sorry for my confusion.

Keep in mind some of my advice could be very dangerous in a book this large, so I’d suggest saving one to two books of the Pentateuch as a sample to work with. My biggest recommendation (and least destructive) would be to set up a style for the last few verses of a chapter, then set up specific character and word spacing rules that fix the problem. Changes to a single verse are too noticeable, but changes to, say, the last three verses can save your skin here.

I think applying manual overrides on 5% of a 1000+ page book is too much work, so what I’d recommend is:
1. SAVE A COPY of just a sample of the book. Any of the books of Moses are long enough to give examples of what you’d risk as you try to fix them. You absolutely do not want to mess with the book as a whole.
2. From there, see if you can find a pattern for the offending pages. It looks like your problem is related to spreads where the facing page begins a chapter. Trouble is this rarely happens (usually chapters start mid-page without a problem).
3. You’ll likely have a specific number of lines missing from the non-matching columns. This may mean any even number, any odd number, or 1-3 lines (the number I find most common). The most common numbers indicate what you’ll need to target in the styles you would create to fix the problem.
4. Adjust a few different style options to see what matches for each offending number. Usually you’ll have a common number to work with, and your advantage here is that Bible verses are usually quite short. Your disadvantage is it looks like you have each verse starting on a new line, which creates some huge problems now.

Sorry that last step is not really a “step” but it’s hard to know without actually having files to mess with. I think a big part of your problem could be a result of unexpected things like your line justify settings (why do your lines have a ragged left margin?) and the math of your baseline grid (11.25 is a difficult number to work with). Not that you can change that, but clearly this is a difficult project.

The good thing is as long as you have this occurring only 5% of the time, that’s 50/1000 pages you’ll have to fix. It’s not as bad as it could be (small consolation) but the offending short pages may be fixable only by setting up specific style rules I can’t look into myself: anything from text styles, to object styles, to case-specific overrides. The best thing I can say is that by creating styles that fix the common errors, you can fix 95% of that 5%.

Sorry for not totally answering your question the first time. I hope this helps more.

I love the book feature whenever I’m working on any larger document. Basically, unless you an excellent and powerful computer, you won’t find it easy to deal with hundreds of footnotes. Repaginating a document that large would allow me enough time to take a coffee break before my computer finished one job.

Now, in smaller documents it’s great to stick with one file. However, since footnotes usually reset themselves after each chapter anyway, and since chapters easily stand as their own sections, it’s much safer to incorporate changes in a book file. Reflowing one line of a 100-chapter book requires a second pass through the entire work if you want to make sure the text no longer shows up on the wrong master page–and don’t get me started on running headers in 100 chapters.

I guess it all depends on your tech and your workflow. If you do a lot of academic publishing or have to deal with anything that has numerous chapters, it’s a ton easier to put each chapter as its own document and (excuse the term) “bookify” it. At least, that’s what I’ve found after typesetting numerous books in a series of academic reprints.