@John_Ha, @Rory_OF, first thank you for the time you have both spent on this, it is a vexing issue for me and I appreciate the help.
That the documents are tangled could certainly be the case, and I agree the documents are rather old, perhaps pre-v4. In any case, footnotes, to my knowledge, do NOT have to appear on the page that they are anchored. If you look at the page style->footnote tab, you can see where you can specify how tall footnotes are allowed to grow on any given page for that style. I think that is supposed to mean that once that limit is reached, footnotes anchored closer to the bottom of the page will get pushed to subsequent pages. I have played with this a lot to see what the editor would tolerate better, even allowing them to grow to maximum height on the page they are anchored I still ran into issues. I do not have an issue with this type of functionality itself, in fact, it should be the desired and expected behavior.
N.B. I have also tried to use endnotes and have had mixed results. The primary problem here is when the next sub-document gets pulled in adjacent to it, if it has a style that injects special page formatting, that seems to get messed up, in most cases, it appears as though it is ignored completely. I have to usually refresh that section to force the editor to retry the formatting, sometimes it works, sometimes it doesn't. Its also good to note here, that I am dealing with large documents, 500+ pages, 50+ sub-documents, 5+ indicies, 300+ images, tables, etc., so running into the odd problem is not totally unexpected.
As you have already tangentially suggested, I am going to suggest the following and please let me know if you think its a good approach, to kind of clean the slate as it were, since it might take a considerable amount of my time to do so, but hopefully prevent you guys from going down a virtual rabbit-hole.
I am going to create a new sub-document template file with the styles I need, page, section, etc., using v4.1.7. This should mean, no old garbage should be included in the file. Once I have done this to my satisfaction, leaving all old styles and other trash behind, I will copy the new template file, so as to keep a backup, and then copy insert the text I have from our current example sub-document file into it, setting the text to the appropriate styles along the way. I will create a new master document using same methodology and then include the new sub-document.
Questions:
- Do I have to create the
same styles in the master document that are in the sub-document? Or, will they by default, get dragged over and set automatically? I was always under the assumption you had to
manually set them to ensure they were in the master document too, correct?
- I do not like styles like default and textbody, so I usually override them, is this a bad idea? Is it a bad idea to have standard style in a sub-document being overridden by a different style in master? Or must the style names always be the same? I do not remember any writer documentation indicating otherwise.
The reason I am asking, I am seeing some weird things trying to use it with the documents I have already provided you, in an attempt to pull some of those styles over into the new (v4) template documents, that I am trying to create as a test. This has to be done manually? 
