It looks like your real work lies in the so-called notes not in the original chapters. Then this does not correspond to the usual definition of notes as short side information to provide marginal information helping to understand the main stuff.
Consequently, your work should be composed as a chapter per se, with sub-chapters matching the original chapters (to avoid confusion main heading for this chapter should be unnumbered, while sub-chapters can keep the original numbers).
If the number of notes per original chapter is rather low, you can obtain what you are looking for through a manual process. BUT, there are two serious shortcomings:
- The process is manual: if you insert a new “note”, you must renumber manually the subsequent notes (hence the remark about the number of notes per chapter).
- I understand you are in the final steps of your work, the suggested procedure requires a full manual reformatting.
The idea is to replace footnotes/endnotes by cross-references.
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Note mark in the original chapter
Type your note reference, say 5 (it is totally under your control). Select the reference, transform it into a bookmark with Insert → Bookmark..., give it a name which may include the chapter number, like 2-5, b5 or anything you like but showing the order of occurrence for ease of later usage, click OK.
With the reference still selected, style it with character style Footnote Anchor (or Endnote Anchor).
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Comment chapter, aka the “notes”
The groups can be automatically subheaded through cross-references with the original chapter number and title. The subheading can even be a Heading 2 paragraph if you want it inserted into the table of contents.
The chapter notes are written (or rather copied/pasted from your initial work) after the subheading paragraph as follows.
Insert a cross-reference, say b5, as Type=Bookmark and Insert reference to=Reference. Select the cross-reference, style it with character style Footnote Characters (or Endnote Characters). Type or paste your note/comment after the cross-reference and a space or tab.
Your note paragraphs should be formatted through a custom paragraph style so that you can easily adjust their look-and-feel to your taste. The lay-out is controlled by:
- the paragraph style for your comments (margins, indent – i.e. separation between note number and text --, etc.)
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Footnote Characters for the comment number (relative size, position)
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Footnote Anchor for the note number in the original text
I am aware that my suggestion implies a lot of manual error-prone work and it is merely a workaround for a non-standard use of notes. If you decide to experiment, backup your original file first.
Please give feedback about the applicability of this idea.