Back from my activity.
There are several issues in your layout.
Layout
I understand your specification for single column notes vs. 2-column main text (aesthetic reasons; didn’t you ask recently about it?). So chose to use a section to enable 2-column main text without forcing simultaneously 2-column notes.
But this results in “crossed” structure. Your notes originate from the section and are set outside the section in the note area of the page. In such a configuration you can’t specify a distance between “text” (section) and the separator and also between the separator and notes (“spacing to contents” which is locked at 0 or 0.1 cm). You lose a lot of control over your layout.
Honestly, I don’t know how to solve the 1-column/2-column dilemma. Writer has no provision for this layout.
Direct formatting
All typographical variations in main text are done with direct formatting instead of character styles. This is the case, for example, for colour of verse numbers. Direct formatting is also reported in your notes though I could not see exactly what.
This is not related to your question but has an impact on performance, contributing both to slow down Writer and to increase file size.
Bad use of U+00A0 NO-BREAK SPACE
There is systematically such a space between the end of a sentence and the new verse number. This is logically incorrect and will cause bad line wraps, preventing a line from being cut before the verse number. If you really want to have NBSP, it should glue the verse number and the next word (to prevent line wrap between verse number and start of verse). Perhaps you copied the text from the internet where ordinary spaces are frequently replaced by NBSPs. You should fix that.
There are NBSP in chapter headings but this is less serious here (only aesthetic impact).
Once again, this is not related to your question.
Tampered heading hierarchy
You apparently want to replace Heading n application by styles of your own. The easiest procedure is rather to customise built-in Heading n.
Creating a custom hierarchy is possible but you must be careful and fully understand what’s going on. In your case, you derived your user styles from Heading 2 but attached both to level 1. You probably noticed problems because you then tweaked Tools
>Heading Numbering
to clear level-2 association.
As your document is presently configured, you won’t be able to use automatic numbering and will have a hard time with the TOC if any.
Too long paragraphs
This is one main problem. Your “chapters” are made of a single paragraph. This is no particular issue in “ordinary” documents (without sections) but becomes really problematic with multi-column sections.
In Writer box model, paragraphs are the basic units. The size of the box is first computed and “pre-chopped” according to present context. And this context is complicated by the presence of out-of-section notes. Writer must do a computation both in the section and in the page, requiring caching processed text.
Your “monster paragraphs” span several pages, putting a considerable stress on memory.
Your first task will probably to check the original text to see where you can add paragraph breaks (I have several editions of the Book and all have several paragraphs per chapter).
This will surely improve global behaviour and fix invisible text on several pages.
As a comparison, I attach a demo document I worked with a few years ago after a question on AskLO (the question was rather about margin notes in addition to footnotes).
ComplexLayoutExample.odt (43.7 KB)